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DU Series 700 User's Guide

1. Store Icon Folder with Arrow stores the scan data amp 645 0 nm Integral 0 142 Reference Off On allows you to select a reference scan ww i ee CI START from the stored scans and overlay the current scans with the reference NOTE This option is available only when there are stored scans and the selected reference has the same wavelength range and steps e lets you enter the wavelength range lower and upper limit as well as the scan resolution or step Select View toggles between Graph scan and Table tabular data NOTE The screen displays Select View after the first scan DU Series 700 User s Guide D PN A24014 AA Wavelength Scan Mode Parameter Setup Options 3 Touch More to go to the previous page of the Options Cursor Mode screen Track Data le i DERIT i Cursor Mode lets you select Track or Peak Valley With off Poule eo Units Track the cursor moves to the next or previous step With Peak Valley the cursor moves to the next or previous peak or valley Send Data sends data to a printer computer and storage device Return yooteu Integral On Off when toggled to On the scan integral is displayed in the bottom left corner of the screen replacing the displayed date Scale amp Units lets you select Absorbance or Transmittance and determine the y axis scaling manual or automatic NOTE For instructions on storing and printing scan data see
2. O seaman COULTER DU Series 700 User s Guide A24014 AA August 2005 Beckman Coulter Inc 4300 N Harbor Blvd Fullerton CA 92834 3100 Copyright 2005 Beckman Coulter Inc DU Series 700 User s Guide Copyright Licenses and Trademarks Copyright Beckman Coulter Inc 2005 All rights reserved No part of this publication may be reproduced transcribed transmitted or translated into any language in any form by any means without the written permission of Beckman Coulter Inc Licenses and Trademarks Beckman Coulter and DU are registered trademarks of Beckman Coulter Inc Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and other countries Table of Contents Section 1 Introduction General Information Proper Use 00005 About this Manual Product Compliance Safety Precautions Electrical Safety 040 safety Against Risk of Fire Chemical and Biological Safety source Lamp Safety Use of Hazard Information Precautionary Labels Waste Management and Recycling section2 System Description oystems and Functions Prep Front and Back View PIS DAY aos depuis eot eder a deesse Tips for Using the Touch Screen Ports and Power 0 Beam Path 0 cee
3. Operation Mode The User Program mode lets you recall saved programs The Fixed Wavelength mode collects data at up to 4 wavelengths You can display the data in absorbance transmittance or concentration The concentration is calculated by a user defined factor or formula The Scan Wavelength mode shows how a sample absorbs light over a range of wavelengths You can use this feature to optimize instrument sensitivity with a given chemistry The screen plots the scan The Kinetics Time Measurement mode records absorbance or transmittance at a single wavelength over a specified time period The SCA mode lets you prepare a standard curve for analyzing samples that contain one component The Protein Assay mode provides a simple procedure to calculate the amount of protein in a sample It contains pre selected parameters for seven common protein assay methods DU Series 700 User s Guide PN A24014 AA Installation Main Menu 3 Table 3 1 Main Menu Soft Key Options Nucleic Acid Analysis The Nucleic Acid mode provides ten methods for DNA RNA and oligonuceotide analyses which calculates nucleic acid absorbance ratios and concentrations Other calculations include molecular weight nucleotide length extinction coefficient concentration and melting temperature Dye Incorporation The Dye Incorporation mode works for single and duo color methods spotted array This works for any dye that gives similar fluorescence wavelen
4. Touch A to enter the desired wavelength Fixer Litas 2b nth Lato XS Ar Am Wavelength s and Formula NOTE For more information on how to set the wavelength s the formula Po and the coefficients or factor see on page 47 400 Cancel OK ERES D Options Touch More to go to the Options screen This screen provides Concentration Concentration Format the following options Off 0 01 Concentration Off On allows you to switch the Reading Made Save as i concentration calculation on or off Also you can choose the a formula and determine factor s for up to 4 wavelengths to calculate the concentrations e Concentration Format sets the number of significant digits for the calculated concentration Instrument Return Setup e Reading Mode toggles between Single and Continuous readings e Save as User Program stores the selected parameters as a user program see User Programs on page 43 e Recall Data see Recalling Data on page 127 e Instrument Setup see Instrument Setup Mode on page 31 46 DU Series 700 User s Guide PN A24014 AA Fixed Wavelength Mode Parameter Setup 5 The Concentration screen lets you switch the concentration Concentration calculation on or off When turned On the Concentration Formula button becomes Concentration Formula enabled and you can touch it to access the Concentration Formula Katha screen which allows you to select a formula The factor s for the
5. 0 300 Abs na 3 500 Abs Cancel OK ig Ss 7 2 Taking the Kinetics Readings Kinetics Time OF MAR 2005 20 13 54 Optians 58 S60 nm To set the run time and interval Touch Time amp Interval in the Options screen Touch the left buttons and enter the Total Time and the Reading Interval using the numeric keyboard Touch the right buttons to choose either Minutes or Seconds Touch OK to confirm the kinetics setup NOTE The Reading Interval must be 10 Seconds or larger The kinetics run can have a maximum of 910 data points To set the scale and unit for the y axis Touch Options More and then Scale amp Units Select Abs or T by touching the radio button Select Auto or Manual scaling With Auto scaling default the screen scales the scan to fit the graph area With Manual scaling you can set the lower and upper limit of the y axis by touching the buttons at the bottom and entering the appropriate values using the numeric keypad Touch OK to return to the Options screen Touch Return to return to the measurement mode Before starting a kinetics run you must blank the instrument After blanking the instrument is ready for the kinetics run To enter Kinetics Time mode 1 2 Touch Kinetics Time mode in the Main Menu Insert a cuvette with a blank solution into the cell holder and close the cell compartment recommended To blank against air use an empty cuvette or
6. The Theoretical Melting Point Tm located in the top right corner DNA only The Concentration in the selected unit displayed in large bold characters The Length Len of the oligo the Dilution Factor DilX and the entered base composition displayed right below the concentration The Extinction Coefficient ExtC and the Molecular Weight MW displayed in the bottom right corner of the screen The following methods have a result screen similar to the one shown here Oligo DNA Short Oligo RNA Short This result screen shows the following The Theoretical Melting Point Tm located in the top right corner DNA only The Concentration in the selected unit displayed in large bold characters The Length Len of the oligo the Dilution Factor DilX and the entered sequence displayed right below the concentration The Extinction Coefficient ExtC and the Molecular Weight MW displayed in the bottom right corner of the screen NOTE For instructions on how to use a Carousel Cell Holder a Sipper or a Peltier Temperature Controller see Carousel Sipper and Peltier Operation on page 117 NOTE For instructions on how to print and store data see Store Recall send and Delete Data on page 125 DU Series 700 User s Guide PN A24014 AA 10 4 Calculations Nucleic Acid Analysis Calculations The following sections describe the calculations used by methods in the Nucleic Acid Analysis mode E
7. 0 0 cee Analysis of SdINDICS s uanmentos dort oa da taces dd caine te ate backs bean AUG UU IS te sae fy scp TT TTE Background Correction and Net Absorbance 0 0 0 ccc eee eee Concentration Calculations 0 0 0 0 cc eee eee Molecular Weight Oligo DNA Long Short 0 0 cee eee DU Series 700 User s Guide Molecular Weight Oligo RNA Long Short 0 0 cee eee 92 Molar Extinction Coefficient Oligo DNA Long 0 0 eee eee 93 Molar Extinction Coefficient Oligo DNA Short 0 0 0 cee ee 93 Molar Extinction Coefficient Oligo RNA Long 0 cee eee 94 Molar Extinction Coefficient Oligo RNA Short 0 0 0 eee 94 Extinction Coefficient Oligo DNA RNA Long Short 0 0 e eee 95 Concentration Oligo DNA RNA Long Short 0 0 cc cece eee eee 95 Melting Temperature Oligo DNA Long seesen n mR eee eee 96 Melting Temperature Oligo DNA Short 0 0 ee nee 96 Section 11 Dye Incorporation Method DS SCI DUO scere erecti por eo etal hse bett Eco et o iofra dese ed 99 Parameter SBEUD sus i iret et merda teaiod gt dha Grd we ri debe sed ered 100 Analysis of Samples sssseeesse een 101 section 12 DNA Protein Tools Mode 3IEHIOMOTIS o canes uis Ue se tenses T E sS RENNES UE E 103 Protein Concentration from Amino Acid Sequence Data 0006 104 Radioactive Decay C
8. 17 3 Upgrading the Instrument Software Fe Update 1 Touch Instrument Update to update the system firmware through the USB connection Please insert an Instrument Update 2 Follow the instructions on the screen and run the update Module inta 4 USB port program nr 3 Touch OK to return to the System Checks screen connect to a computer that is runing the update program Cancel OK 17 4 Optical Checks Optical Checks Touch Optical Checks in the System Checks screen Wavelength Noise Check Check From the Optical Checks screen you can execute a number of Stray Ligth M SMS performance tests These tests are described in the following Check Chec sections Drift Check 152 DU Series 700 User s Guide PN A24014 AA Wavelength Check Wavelength 656 1 nm Lamp Warmup cancel Start 0 tic i7 Ls n ale Wavelength Check Wavelength 656 1 nm Peak 656 0 0 636 nA Bandwidth 7 0 cancel Start A DU Series 700 User s Guide PN A24014 AA System Check Optical Checks l vi The Wavelength Check test lets you verify wavelength accuracy at 656 1 or 486 0 nm When you select 656 1 nm the test also reports the bandpass at 656 1 nm 1 Touch to select the wavelength 2 Makea choice and confirm with OK 3 Touch Start NOTE This might take awhile if the lamp is not warmed up sufficiently In this case the Lamp Warmup message appears informing you that
9. B 1 n Blank Blank R 1 n Read Read B 1 Blank amp Read Blank amp Read R 2 n B 1 3 5 Blank amp Read Blank amp Read R 2 4 6 B z Blank cell position R Sample cell position n number of samples in the Carousel Fixed Wavelengths Measurements Fixed Wavelength 800 nm Cell Abs 1 29 SEP 2004 09 34 06 bh Options DU Series 700 User s Guide PN A24014 AA This section applies to Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes Touch Blank or Blank amp Read to start the first set of measurements The status bar displays the instrument operation Reading Blanking while the Carousel turns and the instrument takes readings as programmed through the Instrument Setup menu 117 Carousel Sipper and Peltier Operation Carousel Holder Fixed Wavelength 29 SEP 2004 11 03 13 Cancel Options Wavelength Scan wavelength Scan 0 000 Abs 450 4 545 0 nm Integral 0 142 b ad Exit Blank amp Read Options 118 After starting the Reading sequence the screen replaces the Blank Read buttons with a Cancel button The instrument lists each reading on the display as it is taken When blanking or reading the position number appears in the Carousel icon see arrow NOTE Touch Cancel at any time to start over and to erase all readings from the current set of measurements After finish
10. Spectrophotometer you need to connect a number of tubes 22 DU Series 700 User s Guide PN A24014 AA Installation Modules 3 To install the Sipper Module 1 Draw the drain tube through the exit channel of the sipper from the inside outwards The push on connectors must be inside the sipper 2 Draw the inlet tube through the entry channel of the sipper from the outside inwards The push on connectors must be inside the sipper NOTE Take care to avoid causing any kinks in the tubes 3 Turn the Sipper Module on its side 4 Draw the inlet tube and the drain tube through respectively the entry channel and the exit channel of the sipper The inlet tube must be drawn through the guide tube The bottom end of the guide tube must click into the channel NOTE Take care to avoid causing any kinks in the tubes 5 Hold the rubber fitting with the ridges over the grooves and push it firmly onto the guide tube and the waste tube DU Series 700 User s Guide 23 PN A24014 AA Installation Modules 6 Make sure the rubber fitting firmly encloses the guide tube and the drain tube Open the cell compartment Without the locking screws insert the Standard Cell Holder or Microcell Holder see Standard Cell Holder Installation on page 14 in the cell compartment Place the Sipper Module on the Standard Cell Holder or Microcell Holder in such a way that the screw holes are positioned exactly one above the othe
11. The bottom left corner of the display shows the Difference between the two scans in absorbance or transmittance Wayricecth ease iii TO set the scan or wavelength Wavelength Range 1 Touch the key in the Options menu 340 900 _ rw 2 Touch the top left button to change the lower limit and enter Step the desired value using the numeric keypad Co o imi a ED aa 3 To set the upper limit touch the top right button and enter the em j C x 0 2 nm zm desired value using the numeric keypad C n 5 nm C 5nm Cancel OK a Hc 3 1 NOTE Do not enter the same value for lower and upper limit When entering a value for the lower limit that is higher than the upper limit or vice versa the values are reversed 4 Select the scan resolution or step by touching the respective radio button Selecting a larger step allows the instrument to scan faster but decreases the resolution of the scan Depending on the selected wavelength range you may select steps between 0 1 and 5 nm NOTE A total of 910 data locations are available for each scan 1100 nm 190 nm 910 ata 1 nm step Intervals that exceed this boundary are automatically grayed out and cannot be selected NOTE Recordings of high resolution scans take longer than recordings of low resolution scans For example 0 1 nm resolution is equal to a speed of 100 nm min while 5 nm resolution is equal to a speed of 4500 nm min A common and practi
12. nm 4 If necessary touch the UV Switch button to select a wavelength between 320 and 360 nm at which the instrument changes from the visible to the UV source Use the alphanumeric keypad to enter the switching wavelength NOTE Usually there is no need to change the default value of 331 nm for the switching wavelength 5 Touch OK to confirm The screen returns to the Instrument Setup menu NOTE A program that requires a lamp has the highest priority If for example the lamp in the Lamp Control screen was turned off but the current program requires the lamp the lamp turns on automatically DU Series 700 User s Guide 35 PN A24014 AA Installation Instrument Setup Mode Fixed Wavelength VO 320 nm Lamp Warmup Agzo j SEP 20 04 14 06 27 lh Cancel Options Fixed Wavelength Ve 320 nm 0 000 n Agzo 0 000 j SEP 20 04 14 10 15 ab Optians USB Port Table 3 2 Connector Ports Connector Description Measuring Mode Effects 1 UV Lamp switches on manually The UV Lamp icon appears flashing in the display 2 The instrument displays Lamp Warmup NOTE For the most accurate and stable measurements in the UV range let the lamp warm up for five minutes before taking the first reading 3 When the lamp is warmed up and ready the UV icon stops flashing NOTE If both lamps are On the symbol UV VIS appears in the selected Measurement Mode NOTE As an alternative you
13. 000 1 0000 length of 1 cm if you want to use small path length cells for e Store Data Off On lets you toggle the storage setting and manually store data e Save as User Program stores the selected parameters as a user program see User Programs on page 43 Instrument Return Setup 82 DU Series 700 User s Guide PN A24014 AA Double Ratio amp Concentration Nucleic Acid Analysis Double Ratio amp Concentration 92 101 som Metso Cones 1 842 50 000 Dilution x 1 0000 09 FEB 2005 17 17 35 Nucleic Acid Analysis U VIS 320 0 nm Double Ratio amp Concentration 2 209 0 485 KEETE hiho Ratio 4 3 Ratio Azzoo Metzana Metzgoo Netzzon 1 567 0 6685 3 232 z50 0 AzBO 0 1 769 0 907 3 455 U 222 09 FEB 2005 17 18 37 FN Optians DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Parameter Setup 10 Touch Options for parameter setup More displays further options in the Options screen View Conc Abs lets you toggle between the result concentration and the raw data absorbance values screen NOTE The first screen shown here with the options menu is the result screen while the second is the raw data screen with background correction turned on Dilution X lets you enter a dilution correction factor The displayed results are corrected for dilution using the following equation Congo Conc x Dilution lets you modify the default wave
14. 10 Nov 04 15 01 52 Scan 3 425 4535 nm 0 5 nm 11 MOo uy D4 14 10 47 Scan 4 423 453 nm 5 0 nm Return Table Graph Options 128 DU Series 700 User s Guide PN A24014 AA Wavelength Scan 620 0 nm V Lew Return Summary Options Wavelength Scan Ej Test Abs Min Max 428 0 0 001 Walley 438 0 0 000 446 0 0 000 PN Optians Meu Return summary DU Series 700 User s Guide PN A24014 AA Store Recall Send and Delete Data Recalling Data Scans and Kinetic Runs l 4 To display the graphical representation of the selected scan example shown on the left touch Graph The button changes to View Summary to let you return to the previous screen If manual scaling has been selected you can use the alphanumeric keypad to set the limits Y nin and Ymax In this case the graph adjusts to display only the scan values in the selected range If automatic scaling has been selected the system sets the limits automatically to display the total scan range To display the tabulated data of the selected scan example shown on the left touch Table The button changes to View Summary to let you return to the previous screen 129 Store Recall Send and Delete Data Recalling Data Scans and Kinetic Runs Recalling Kinetic Data Kinetics Time To recall kinetic data touch Recall Data from the Main Menu and then Kinetics Time The screen displays a list of stored kinetic 13 96 30 runs if
15. DNApmo1 x 660pg pmol x N ug 106pg x N DNAng DNA pmo x 660pg pmol x N ug 109pg x N where DNAyg Result dsDNA in yg DNA Result dsDNA in ng DNApmoi dsDNA in pmol N Number of nucleotides The average molecular weight of nucleotides is 660 pg pmol 109 DNA Protein Tools Mode Conversions Micrograms mL of Oligonucleotides ssDNA to Picomoles pL This function converts oligonucleotide ssDNA concentrations ug ml to pmol uL The following parameters must be supplied e Length of Oligo in nucleotides e Concentration in ug ml Equation Oligopmoyy OligOygimi x MI 1 000 pmol 330pg x 109pg ug x 1 N where Oligopmoyy Result Oligo in pmol ul Oligo gj Oligo in pg ml N Number of nucleotides The average molecular weight of nucleotides is 330 pg pmol Picomoles yL of Oligonucleotides ssDNA to Micrograms mL This function converts Oligonucleotide ssDNA concentrations pmol uL to ug ml The following parameters must be supplied e Length of Oligo in nucleotides e Concentration in pmol ul Equation OligOugimi OliGOpmotpi X 1000pI ml 330pg pmol x ug 106pg x N where Oligouygjm Result Oligo in pg ml Oligopmoyu Oligo in pmol ul N Number of nucleotides The average molecular weight of nucleotides is 330 pg pmol 110 DU Series 700 User s Guide PN A24014 AA DNA Protein Tools Mode Conversions l 2 Micrograms of Linear DNA to Picom
16. Factor Pathlength 3 where Net Abs Net absorbance at 260 nm calculated using equation 1 Conc Factor Concentration factor user input 91 Nucleic Acid Analysis Calculations Molecular Weight Oligo DNA Long Short Molecular Weight Oligo RNA Long Short 92 Dil Factor Pathlength Dilution factor user input jn cm user input NOTE These concentrations are calculated using the net absorbance at 260 nm However you may change the wavelength if you do you must also change the concentration factor since the extinction coefficient is a function of wavelength The system calculates the molecular weight of DNA oligos from the input base composition of sequence using the following equation MW MW x da MWc X dC MWg x dG MW x dT MWN x dy 18 02 4 where MW Molecular weight of adenine 313 2 g mol dA Number of adenine bases user input MWc Molecular weight of cytosine 289 2 g mol dC Number of cytosine bases user input MWg Molecular weight of guanine 329 2 g mol dG Number of guanine bases user input MWy Molecular weight of thymine 304 2 g mol dT Number of thymine bases user input MW Average molecular weight of A C G T at 308 95 g mol dN Number of unspecified bases user input The system calculates the molecular weight of RNA oligos from the input base composition of sequence using the following equation MW MW x dA MWc X dC MW
17. Setup menu DU Series 700 User s Guide 123 PN A24014 AA Carousel Sipper and Peltier Operation Peltier Module 124 DU Series 700 User s Guide PN A24014 AA 14 1 Storing Data Storing Data Auto Manual Fixed Wavelength 400 cog So Tans 20 SEP 2004 08 24 45 wr Optians DU Series 700 User s Guide PN A24014 AA Store Recall Send and Delete Data Storing Data 14 Store Recall Send and Delete Data DU 700 Series instruments can store up to 1000 readings taken in the most modes Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation In Wavelength Scan mode the instrument can store up to 20 scans The Kinetics Time mode stores up to 20 kinetic runs This section applies to Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes You can set the instrument to store the data automatically Store On or store data manually at your discretion Store Off Single Reading Mode When the Options menu displays the Store Off button the instrument does not automatically store readings To print the data or save it to a memory device the readings must be stored until the set of data is complete The data can then be printed or sent to a memory device using the Data Recall function Therefore it is recommended to store your data To store specific data manually set the Store button to Off After taking the reading set
18. Store Recall Send and Delete Data on page 125 Select Reference Scan To recall stored scan data to be used as a Reference Scan for 22 DEC 4 09 27 08 overlays Scan 1 340 900 nm 41 0 nm 1D DEC D4 11 59 21 1 From the Wavelength Scan mode touch Options scan 2 400 1000 nm 4 5 0 nm 10 DEC 04 11 59 21 2 Touch Reference Off Scan 3 400 1000 nm 4 5 0 nm D3 DEC D4 11 20 31 3 In the Select Reference Scan screen touch the line with the Scan 4 SOO 600 nm 5 0 nm 3 DEC d 16 75 58 Scan 5 FOO 600 nm 5 0 nm desired Scan to highlight it 4 Touch Highlight Reference or Highlight Data Reference Highlight Highlight Cancel Off Reference Data 52 DU Series 700 User s Guide PN A24014 AA Wavelength Scan Mode Parameter Setup 6 The system returns to the scan mode showing the Reference Scan as an overlay if a scan has been taken already The button in the Options menu now indicates Reference On Reference Scan The Reference Scan is shown in gray and the Measured Scan in black NOTE This option can display only scans that have the same wavelength range and resolution 620 0 nm A black and a gray box in the top left corner of the screen Difference 0 756 i identifies the scan for which the cursor is active Exit Blank Options Touch the black or gray box in the top left corner to switch the cursor from the measured scan to the reference scan and vice versa
19. Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes l0 recall stored data touch Recall Data from the Main Menu and acetate then Data Log The screen displays a list of stored data if 2e DEC 04 09 23 01 available as shown on the left 0 027 Abs Fixed ESI E a A When you touch View Details the screen displays complete PEE information for the selected sample The button changes to View 0 387 Abs Fixed X Summary to let you return to the previous screen geo 3025 0 363 Abs Fixed A 22 DEC U4 09 23 28 0 338 Abs Filter VL ew Off Details Options Return DU Series 700 User s Guide 12 PN A24014 AA Store Recall Send and Delete Data Recalling Data Scans and Kinetic Runs To filter out desired data use the Filter On Off button With the filter activated you may select any combination of the following options Filter e Sample ID Sample ID Operator ID e Operator ID Test PG e Start Date Start Date Parameter 12 NO0V 2004 Fixed A e Parameter Touch OK to filter the stored data based on the settings P Cancel OK RSS EN Recalling Scans Wavelength Scan To recall stored scans touch Recall Data from the Main Menu and then Wavelength Scan The screen displays a list of stored scans if available as shown on the left Wavelength Scan 2f OCT O4 17 55 55 scan 1 425 453 nm 4 5 0 nm 29 OCT 04 16 54 00 Scan 2 423 453 nm 5 0 nm
20. You can use the DU Series 700 for testing samples in the visible and ultraviolet wavelength spectrum A halogen gas filled tungsten lamp produces light in the visible spectrum 320 to 1100 nm and a deuterium lamp produces light in the ultraviolet spectrum 190 to 360 nm The DU Series 700 Spectrophotometer provides digital readouts in Absorbance or Transmittance as well as calculated units depending on the mode USB ports for printer keyboard and memory devices are standard DU Series 700 User s Guide 5 PN A24014 AA System Description Design When you select a user generated or programmed method the on screen menus and prompts direct you through the test You can also use these menus to generate reports run statistical evaluations of generated calibration curves and report instrument diagnostic checks 2 2 Design Front and Back View Figure 2 1 Front and Back View Display The display is a touch screen device and the content changes as you select different modes of operation Figure 2 2 shows the two main menu screens with the available application programs of the DU 730 6 DU Series 700 User s Guide PN A24014 AA System Description Design 2 Figure 2 2 Main Menu Screens lain Menu Main Henu Fixed Wavelength Un Dye Incorporation DNA Protein Tools Wavelength Scan Kinetics Time Return Single Component System Instrument System Recall Instrument Checks Setup Checks 77 Data Setup Tips fo
21. a Touch Carousel Options in the Instrument Setup menu Touch Carousel Off to change its display to Carousel On c Touch OK to confirm your selection 2 Setthe carousel options a Touch Carousel Options and touch Select the carousel option of your choice For example the first option is Blank 1 Read 1 7 which means that the blank cuvette will be read in position 1 while samples must be placed in the cell positions 1 7 With this option you must remove the blank cuvette after blanking c Use the arrow keys to specify the number of cell positions you want to use 3 Touch OK to confirm and return to the Instrument Setup menu NOTE As an alternative you can access the Carousel Options screen directly from the measurement mode by touching the Carousel Icon on the bottom right of the screen The Carousel Options screen appears and you can quickly make the necessary changes DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 Sipper Module Instrument Setup If your instrument includes a Sipper Module the Instrument Setup Operator ID Sample ID menu provides Sipper Options You can modify the sipper lt OTf gt i lt OTf gt parameters using this menu Date amp Display amp Time Suina 1 Touch Sipper Options in the Instrument Setup menu to Lamp E S display the Sipper Options screen Control p d Sipper assuor iine Return Instr set 6 6 2 Modify the desired parameters f
22. assign the Operator ID to a measurement from the measurement screen or the Operator ID menu This feature helps record which operator measured each sample To create an Operator ID 1 Touch Operator ID in Instrument Setup mode 2 Touch New to enter a new Operator ID anaes 3 Use the alphanumeric keypad to enter a new Operator ID see Operator ID Alphanumeric Keypad on page 30 N NOTE Use the alphanumeric keypad to enter a new Operator ID You abc ABC DEF GHI GE cannot use spaces in this function Use underscore symbols instead YZ Key e o MNO POR NOTE Touch Delete to remove an Operator ID from the list 123 sm vwx vz_ p Cancel OK DU Series 700 User s Guide 31 PN A24014 AA Installation Instrument Setup Mode Instr eens ant CF Operator ID ADGMI Instr eee oat OF ee Sample ID Instr pees oat CF ee et Sample ID Cancel OK 32 4 Touch OK to save your changes The screen returns to the Instrument Setup menu and shows the selected operator identifier NOTE If an Operator ID is active you can also touch the Operator ID icon directly on the Measurement screen The Operator ID screen opens in which you can change the ID Use the Sample ID screen to enter up to 30 sample identification tags up to 13 characters each into the instrument You may want to use this to identify the samples more effectively To access this function 1 Touch Sample ID in
23. available as shown on the left Kinetics Time 14 00 40 S70 nm 15 NOV 04 16 07 16 Run 3 570 nm 15 07 18 Run 4 570 nm Return Table Graph Options To display the graphical representation of the kinetic run example shown on the left touch Graph Kinetics Time The button changes to View Summary to let you return to the previous screen 0 500 min Return Options 130 DU Series 700 User s Guide PN A24014 AA Store Recall Send and Delete Data Sending Data Scans and Kinetic Runs l 4 To display the tabulated data of the selected kinetic run example K neti cs TI ne Recall Data Em NE WM Shown on the left touch Table mi The button changes to View Summary to let you return to the g y previous screen VELEIA ih Return Summary Options 14 3 Sending Data Scans and Kinetic Runs sending Data This section applies to Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes You can send data to a printer or a memory device using the Send Data available USB ports Since the system automatically senses connected devices it sends the data to all available devices Single point To send data C Filtered data 3 ob pr 1 Touch the Options button am C All data 88 2 Touch Send Data USB Port icon The Send Data screen displays enabling you to send a single point selected item the filtered data or all data to the desired
24. cON4 ug 15 07 Nucleatides pmoal This screen shows the results for one color only To see the results Amount prnol for the second color Cy5 touch Options and then Cy5 hz amp no zman ssoo ssoo Conc pmM Selecting this option toggles the result screens between Cy3 and Cy5 0 250 0 751 0 181 0 005 Mass uag Ratio Pc O9 NOWw 2004 13 35 03 ii Options 102 DU Series 700 User s Guide PN A24014 AA DNA Protein Tools Mode Calculations l 2 DNA Protein Tools Mode The DNA Protein Tools do not measure samples Instead these tools or functions are available to help you with your daily laboratory tasks The tools provide calculations common conversions and a number of common tables from the microbiology handbook DNA Protein Tools To enter the DNA Protein Tools mode touch DNA Protein Tools Tables in the Main Menu Cancel 12 1 Calculations In the Calculations screen touch the desired button to perform the Calculations function Concentration Decay Touch Cancel to return to the DNA Protein Tools screen NOTE When entering a function a results screen without values may appear When this happens touch Options first and enter or change the parameters before touching Calculate to calculate and display the result s Cancel DU Series 700 User s Guide 103 PN A24014 AA DNA Protein Tools Mode Calculations Information Gill 5 C von Hippel P H Calculation of protei
25. compartment DU Series 700 User s Guide 25 PN A24014 AA Installation Modules 2 Insert the Peltier Module in the cell compartment with the module lid open toward the back of the instrument see Figure 3 16 3 Secure the Peltier Module with two locking screws Figure 3 16 Installing the Peltier Temperature Control Module 26 DU Series 700 User s Guide PN A24014 AA 3 4 Switching the Power On Language Selection Main aa Language English Deutsch Self Check a DU 730 Self Check E SYSTEM TESTS E LAMP TESTS CALIBRATION A FILTER ADJUSTMENT wc VOLTAGE TESTS Nuc Please keep lid closed i DU Series 700 User s Guide PN A24014 AA To switch on the instrument 1 Close the cell compartment 2 Press the power switch on the back Installation Switching the Power On 3 WARNING Do not switch the instrument off and on in rapid succession Always wait about 5 seconds before switching the instrument on again otherwise you may damage the electronic and mechanical systems The software of the DU Series 700 Spectrophotometer includes several language options To choose a language 1 While turning on the instrument touch the display until the screen displays the list of languages 2 Select the desired language 3 Touch OK to confirm the language selection The self check starts automatically NOTE The instrument continues to power up using the selected language until you sele
26. concentration calculation are also determined in this screen Unit mg L together with the A selection Touch the Unit button to select a concentration unit or add a new unit to the pre defined units You may delete only user defined units NOTE The selected unit is not shown unless a concentration is calculated in this case the factor must be other than 1 0000 and or a formula other than 4 a1 has been selected Touch OK to save the parameter setup The following formulas are available Ky Aj K Ay Ky Ad KATK Ase As K A Ky A gt K A Ky Ay Kj Ay Ky A5 K3 A3 Ky Ay Ky Ag K3 A3 K4 Ag A refers to the absorbance at wavelength 1 A refers to the absorbance at wavelength 2 etc K refers to the coefficient at wavelength 1 K refers to the coefficient at wavelength 2 etc Coefficients can be set negative where subtraction is required e To change the formula touch the button that displays the pu Wavelength s and Formula current formula e To change a wavelength touch one of the Ax keys e To change a coefficient touch one of the Ky keys E K1A4T Kz2 z2 KaAa Enter the desired wavelength s and or coefficient s with the 11 Az Az 400 S00 enun numeric keypad and touch OK EY Ez Ez diio diio diio NOTE The instrument allows you to enter up to 5 significant digits with a maximum of 4 significant digits after the decimal point de
27. ee source Compartment Unpacking the Instrument Operating Environment Power Up Applying Power Section 3 Installation Cell Compartment Cell Holders 0 0 Standard Cell Holder standard Cell Holder Installation 50 uL Single Cell Holder 50 uL Single Cell Holder Installation Turbidity Cell Holder Turbidity Cell Holder Installation Multicell Holder 000 Multicell Holder Installation Carousel Holder Sample Changer DU Series 700 User s Guide Carousel Holder Installation 0 0 eee eee 18 MOGULS V 19 SPPE EMO GUC Bite tert hieer tome aed near aaa ase ees 19 oipper Module Installation 0 0 00 ee eee eee 21 Peltier Temperature Control Module 0 0 0 een 20 Peltier Temperature Control Module Installation 0 0000 20 Switching the Power On 2 cee 21 Language Selection inne tae eae nee a 21 Ser RENTRER a N E A A EART 21 KUNNON se oreu E a E A EEE 20 Alphanumeric Keypad lusssssennn n n RR 30 Instrument Setup Mode 0 0 0 ccc RB 31 GAO COND sacs Sioa ara eas heat eit aso Gare kash one aedi ptos koi Genta AE ptos LEA 31 SOMA rM 32 Date dna TII s omui eco aeta or tou ito ie SUD o TUE UR dde BE eens warded 33 Display and Sound Preferences 0 0 cc cece eee eee eee e
28. graph three buttons allow you to navigate the scan e Peak Valley Touch the top button to toggle between the Track and Peak Valley button that includes arrows cursor modes NOTE You can select the default cursor mode in the Options screen e Left Right arrow buttons The two arrow buttons in the vertical menu move the cursor left and right to the next or previous data point Track or the next or previous peak or Options valley Peak Valley mode A 675 0 nm ZSSSEPAZDUS 14 36 02 The wavelength at the cursor position is highlighted at the x axis of the graph and the corresponding Abs or T is highlighted on the y axis NOTE You can also move the cursor by directly touching on the displayed graph To zoom in or out touch the Zoom Symbol on the left side of the screen Zoom enlarges the area around the cursor position Touch the Zoom Symbol again to return to the former scale NOTE For instructions on using a Carousel Cell Holder a Sipper or a Peltier Temperature Controller see Carousel Sipper and Peltier Operation on page 117 NOTE For instructions on printing and data storage see Store Recall send and Delete Data on page 125 56 DU Series 700 User s Guide PN A24014 AA Kinetic Time Mode Parameter Setup 1 Kinetic Time Mode The Kinetic Time mode lets you collect data in either absorbance or transmittance for a user defined length of time After collecting the data you can display the kine
29. perform than the Lowry assay The standard assay has an applicable protein concentration range of 20 to 1 200 g ml The micro assay has an applicable protein concentration range of 0 5 to 20 g ml When working in the full range a non linear standard curve calculation is suggested DU Series 700 User s Guide PN A24014 AA Protein Assay Analysis Parameter Setup 9 2 Parameter Setup Bradford VIS 595 0 nm To enter the Protein Assay Analysis mode touch Protein Assay Analysis in the Main Menu e Touch Standard Curve if you want to create a standard curve by measuring standards with known concentrations For details see Standard Curve Setup below e Touch Coefficients if you want to enter the coefficients from a previous standard curve For details see Coefficients Setup on page 74 Standard Curae Coefficients Cancel Standard Curve Setup Standard Curve Setup Use the Standard Curve Setup screen to set the parameters Standards Setup Standards Setup allows you to enter the concentrations for TESTE each standard This also determines the number of data nits Concentration Format i mg mL 0 01 points you will have for the standard curve 5 7 scripturam lets you enter the wavelength and turn background correction off default or on NOTE The appropriate wavelength is set automatically for the selected assay It is recommended not to change this default wavelength unless Return as b you ar
30. previous page in the Options menu Dyes lets you choose between 1 color Cy3 or Cy5 and 2 colors Cy3 and Cy5 NOTE When you change the dye selection the system resets the corresponding wavelengths for the dye s to its default values Volume pL lets you enter the desired volume in uL Path Length cm allows you to modify the default path length of 1 cm for the cuvette The 50 uL Microcell which is strongly recommended has a path length of 1 cm Store Data Off On toggles the storage setting from Off to On Save as User Program lets you enter the number for data storage and recall see User Programs on page 43 DU Series 700 User s Guide PN A24014 AA Jo Dye Incorporation Analysis of Samples l sep lo modify the default wavelength and or to toggle the 260 280 Wavelength Options i ratio On or Off touch to go to the Wavelength Options screen T het m Touch 44 to to change the default wavelengths settings and S9 3 SERIES d Pea enter the desired wavelength using the numeric keypad i pea ae NOTE If you chose to take readings for only one dye the wavelength button for the other dye color is grayed out With the selection of 2 colors represents the wavelength for Cy3 and s represents the wavelength for Cy5 The Ratio button toggles the reporting of the 260 280 ratio between Off and On With the ratio turned on you can also modify A4 if necessary OD D jem Tennent a uto M
31. purge is set up for a manual start the instrument waits for you to touch Purge e In the automatic mode the purge begins immediately after the reading without operator intervention At this time if the sample is going to waste you can place a demineralized water purge at the sample inlet to rinse the sample cell between readings Leave the inlet tube in the purge solution until the Sipper pump Stops The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date NOTE If you need to stop the purge cycle during the purge interval touch Cancel 121 Carousel Sipper and Peltier Operation Sipper Module Kinetics Time Kinetics Time Sipping 3 sec 122 S70 mm Options When the sample purge is complete the instrument is ready for the next sample Place the sample inlet tube into the blank solution and touch Blank or Read Leave the inlet tube in the blank solution or the sample vessel until the Sipper pump stops and the settling cycle begins After starting the sipping reading sequence the screen replaces the Blank Read buttons with a Mark and a Stop button NOTE If you need to stop the sip cycle touch Stop The instrument skips the sip and settle cycles The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date When the settling cycle is complete the screen displays the Blank button e Ifth
32. same time The following parameters must be supplied e Absorbance at 260 nm e Type of DNA dsDNA ssDNA RNA or Oligo Equation conc abs g x factor where conc Result Concentration absogg Absorbance at 260 nm factor Concentration Factor see listing below Common concentration factors dsDNA 50 SSDNA 35 RNA 40 Oligo 20 112 DU Series 700 User s Guide PN A24014 AA DNA Protein Tools Mode Conversions l 2 This function performs a couple of molar conversion for proteins Protein Molar Conversion The following parameters must be supplied Parameter Set 1 e Protein Size in kDa e Amount of Protein in pmol Converts to ug of Protein or Parameter Set 2 e Protein Size in kDa e Amount of Protein in ug Converts to pmol of Protein or Parameter Set 3 Amount of Protein in pmol e Amount of Protein in ug Converts to kDa Protein Size Equations Parameter Set 1 protyg Sizeypa X PrOtpmol X 109 x 1 1012 Parameter Set 2 Protpmol PrOtyg sizeypa x 1 109 1012 Parameter Set 3 SiZeypa PrOtyg PrOtpmol x 1 109 101 where Sizeyp4 Protein Size in kDa proto Protein Amount in pmol protug Protein Amount in pg DU Series 700 User s Guide 113 PN A24014 AA DNA Protein Tools Mode Conversions Protein Coding Capacity This function encodes Amino Acids calculates the size of the DNA and predicts the size and len
33. screen The Temperature Control screen appears and you can quickly make the necessary changes 42 DU Series 700 User s Guide PN A24014 AA User Programs Storing a User Program 4 User Programs The User Program mode provides access to programs or modes that have been defined by the user s A user program is one of the application modes with customized parameters The instrument can store up to 50 user programs 4 1 Storing a User Program After selecting the analysis parameters in many off the modes you can store the parameters for later recall NOTE Wavelength Scan and Kinetics Time parameters cannot be saved as a User Program 1 Set the desired analysis parameters in the mode of your choice e Fixed Wavelength Touch Options then More see Parameter Setup on page 45 e Single Component Analysis Touch either Standard Curve or Coefficients see Parameter Setup on page 61 e Protein Assay Analysis Touch Start then either Standard Curve or Coefficients see Parameter Setup on page 71 Nucleic Acid Analysis Touch Start Options then More see Parameter Setup on page 81 e 96 Dye Incorporation Touch Options then More see Parameter Setup on page 100 2 Touch Save as User Program 3 Enter a user Program Number between 950 and 999 and touch OK NOTE If you enter a program outside this range the instrument beeps and displays the next available number If you enter a Program Number t
34. selected scaling mode e Activates the cursor functions in the vertical navigation bar DU Series 700 User s Guide 59 PN A24014 AA Kinetic Time Mode Analysis of a Kinetic Run Kinetics Time 540 0 nm 0 500 min e2e DEC 2004 09 45 27 Optians Kinetics Time 560 nm 0 070 Abs 0 500 min Slope 0 034 r 0 997 Optians 60 After completing a Kinetics Time run the instrument displays a graph of absorbance versus time The graph shows one cursor which is the Elapsed t elapsed time cursor mode Located at the right side of the kinetic profile three buttons allow you to navigate the kinetic data e Cursor Mode Touch the top button to toggle between the Elapsed one point and the Delta At second point cursor mode e Left Right Arrows The two arrow buttons on the vertical menu move the cursor to the next or previous time point The time at the cursor position is highlighted at the x axis of the graph and the corresponding Abs is highlighted on the y axis NOTE You can also move the cursor by directly touching on the displayed graph e Zoom Symbol To zoom in or out touch the Zoom Symbol on the left side of the screen Zoom enlarges the area around the cursor position Touch the Zoom Symbol again to return to the former scale To determine the rate or slope toggle to the Delta At cursor mode with the top button on the vertical menu In this mode you can use the previous cursor posi
35. the system is warming up the lamp to achieve the best results When complete the instrument takes the readings and displays the results 4 Touch Cancel to return to the Optical Checks screen 153 System Check Optical Checks Optic Pa ee P Optic I7 ed oe 154 Noise Check Noise Check Wavelength 540 0 nm Noise Check Noise 0 000 Abs Average 0 000 Abs Std Deviation 0 0000 Abs Sample 0 95172 n Average 0 9492 N Stray Light Check Wavelength 340 0 nm 0 009 Abs cancel Start The Noise Check test lets you test the photometric noise in the instrument The noise is specified at 546 1 nm at 0 0 A However you can also use this to test noise at any wavelength and at an absorbance level determined by a sample 1 Touch A to enter the wavelength 2 Enter the wavelength using the numeric keypad and confirm with OK 3 Touch Blank 4 After the system has blanked touch Start When the test is complete the screen displays the results The instrument averages thirty readings for the blank and calculates the Average and Standard Deviation from 100 consecutive absorbance readings e Noise e Sample e Reference 5 Touch Cancel to return to the Optical Checks screen The Stray Light Check lets you measure the stray light in the instrument at 220 nm or 340 0 nm This test requires user prepared samples The test at 220 0 nm requires a 10 g L Sodium Iodide Nal aqueous solu
36. the Instrument Setup menu 2 Touch New and enter a new Sample ID e Ifyou want to subdivide the Sample ID with numbers touch Add Number e Use the arrow keys to specify how many numbers can be added for the sample identification Touch the key between the arrow keys to add directly the number of choice Use the alphanumeric keypad to enter a new Sample ID see Alphanumeric Keypad on page 30 NOTE You cannot use spaces in this function Use underscore symbols instead YZ key 3 Touch OK to confirm The display shows the chosen Sample ID as shown in the following illustration NOTE Touch Delete to remove a Sample ID from the list DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 Insip oo ert 4 Touch OK to save your changes The screen returns to the Sample ID Instrument Setup menu and shows the selected sample identifier NOTE Ifa Sample ID is active you can also touch the Sample ID icon directly on the Measurement screen to change it The Sample ID screen opens in which you to change the Sample ID eee Use the Data amp Time screen to set the instrument s data and time Date amp Time 1 Touch Date amp Time in the Instrument Setup menu The screen provides the fields necessary to set the date and time 2 Touch the appropriate field and use the arrow keys to change TimetrzdHaur the value a7 a ow a 3 Touch OK to confirm The screen returns to the Instrum
37. the Store button to On to store the reading result The system briefly displays the message Data stored You must then toggle back to Store Off otherwise the consequent readings are stored automatically To store data automatically toggle the button to Store On automatic storage When you then touch Read the instrument reads the sample places the reading result automatically in the data log and briefly displays the message Data stored NOTE When the instrument s memory data log is full the instrument automatically deletes the oldest data allowing space to store new data 125 Store Recall Send and Delete Data storing Data Continuous Reading Mode You can touch the Store icon folder with arrow in the Options menu at any time to place the current reading result into the data log The system briefly displays the message Data stored Fixed Wavelength 20 SEP 2004 19 38 11 Storing Scans Wavelength Scan TEETE After the scan s have been taken touch the Options button and Wavelength scan then the Store icon folder with arrow er QUCT U4 17 55 55 Scani 423 453 nm 5 0 i i E Pu pu The Store Data screen displays Touch the line Scan where you 29 OCT 04 16 54 00 tr ON E want to store the first and maybe only scan and then touch the 10 NOV D4 15 01 52 Store button with the folder icon to place the scan s in storage Scan d 423 453 nm 0 5 nm l1 NOV 4 14 01 29 NOTE Af
38. the default background wavelength Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings 87 Nucleic Acid Analysis Analysis of Samples Options Dilution Salt Concentration 1 0000 50 000 Units Path Length cm pmaol uL 1 0000 Store Data Save as Off 7 User Program Instrument Setup Muci Bete 2 shee ie pia To CN Edit Sequence ER REESE ESA LLL Cancel OK ee 7 10 3 Analysis of Samples 88 E X Touch More to go to the Options screen e Dilution X lets you enter a dilution correction factor The displayed results are corrected for dilution using the following equation Congo Conc x Dilution e Salt Concentration lets you modify the default salt concentration using the numeric keypad Units toggles between the calculation and display of the concentration units pgmol uL and ug mL e Path Length cm allows you to modify the default path length of 1 cm if you want to use small path length cells for very high sample concentrations e Store Data Off On lets you toggle the storage setting and manually store data e Save as User Program stores the selected parameters as a user program User Programs on page 43 In the Edit Sequence screen touch the desired base buttons and enter the sequence of your sample e CE clears the current sequence e Left Arrow f
39. to select the curve fit Spel Define Coefficients and enter the known coefficients a and b for a linear fit and a b E and c for a non linear quadratic fit To use this screen pi Linen ei ni C 1 Touch Linear Non Linear and select the desired curve fit equation STEP Ese d 2 Touch each of the enabled buttons a b c and enter the respective coefficient using the numeric keyboard 3 Touch Done when the setup is complete ancel A standard curve is now available and you can measure unknown samples and calculate the concentrations 74 DU Series 700 User s Guide PN A24014 AA Protein Assay Analysis Reading Standards O 9 3 Reading Standards Bradford TTE XE fter you have entered the concentrations for the standards the Read Standards system is ready to read the standard cuvettes mg mL Met 1 Inserta cuvette with a blank solution into the cell holder and close the cell compartment recommended To blank against air use an empty cuvette or leave the cell holder empty NOTE If the lid of the cell compartment is open the instrument disables the Blank Read buttons uS M cid 2 Touch Blank to blank the instrument The screen displays the Blanking message in the bottom left corner of the screen Bradford VIS 595 0 nm 3 When the system has been blanked insert the first standard Read Standards cuvette into the cell holder and close the cell compartment mg mL Met 0 1500 0 265 4 Touch
40. user input Molar Extinction Coefficient Oligo DNA Short DU Series 700 User s Guide PN A24014 AA For oligonucleotides shorter than 30 bases the base order affects the molar extinction coefficient to the extent that the simpler formula for long oligos does not provide an accurate determination To calculate the molar extinction for shorter oligos you must enter the sequence The system calculates the molar extinction coefficient Apc xyx at 260 nm in units of L umol cm using the equation ABC XYz 2 X eag c Exy eyz p tect x y x 10 3 7 where 93 Nucleic Acid Analysis Calculations EAB Millimolar extinction coefficient for each base pair A Millimolar extinction coefficient for each base Molar Extinction Coefficient Oligo RNA Long For oligonucleotides longer than 30 bases if the number of each type of base is known the molar extinction coefficient Eoligo at 260 nm in units of L umol cm is calculated using the equation toligo cA X dA sc x dC ec x dG zy x dU en x dN x 10 3 8 where c4 Millimolar extinction coefficient of adenine 15 41 dA Number of adenine bases user input ec Millimolar extinction coefficient of cytosine 7 2 dC Number of cytosine bases user input eg Millimolar extinction coefficient of guanine 11 5 dG Number of guanine bases user input ey Millimolar extinction coefficient of ur
41. 105pg ug 1 N where DNApmoi Result dsDNA in pmol DNAyg dsDNA in ug N Number of nucleotides The average molecular weight of nucleotides is 660 pg pmol 108 DU Series 700 User s Guide PN A24014 AA Conversions ug af dsDON4 to pmol pmol of dsDMA 75 7576 Calculate Options Information Gill S C van Hippel P H Calculation of protein extinction coefficients from amino acid sequence data Anal Biochem 182 319 326 1969 DNA Protein Tools Mode Conversions 12 Example for Conversion Functions To enter a function 1 Select ug of dsDNA to pmol or the desired function in the Conversions menu 2 Touch Info to display the available information for this function 3 Touch Calculate to perform the conversion and display the result s based on the parameters set in Options 4 Touch Options to set the parameters for the calculation 5 Touch the parameter that identifies the value you want to change and set a parameter either by e using a numeric keypad to enter a value or selecting the radio button that displays the desired value NOTE Operation of the other functions in this section is similar Picomoles of dsDNA to Micrograms and Nanograms DU Series 700 User s Guide PN A24014 AA This function converts the amount of dsDNA pmol to ug and ng The following parameters must be supplied e Length of DNA in base pairs e Amount of dsDNA in pmol Equation DNA g
42. 2949 USB Printer Cable Table 19 9 Replacement Parts and Supplies A23 8 Halogen Lamp Replacement Kit A23 92 Deuterium Lamp Replacement Kit A23 2 Fuse Time Delay 250V 2 5A Table 19 10 Replacement Parts for Sipper Sampling Module A24209 750 uL Flow Cell A23800 Flow Cell Tubing Kit inlet and waste A23801 Peristaltic Pump Tubing Kit set of 4 586656 Waste Bottle Table 19 11 Trace Klean M Solution 589784 Concentrated 946 mL 598190 Dilute 473 mL DU Series 700 User s Guide PN A24014 AA Replacement Parts Service Centers and Warranty Repair Service Beckman Coulter Sales and Service Offices O Table 19 12 User s Guides A24014 DU Series 700 User s Guide English A24015 DU Series 700 User s Guide French A24016 DU Series 700 User s Guide Italian A24017 DU Series 700 User s Guide German A24018 DU Series 700 User s Guide Spanish A24019 DU Series 700 User s Guide Japanese 19 2 Repair Service Beckman Coulter Sales and Service Offices Technical support and service in the United States Beckman Coulter Inc 4300 N Harbor Boulevard P O Box 3100 Fullerton CA 93834 3100 Tel 800 742 2345 Fax 800 643 4366 For up to date information on offices worldwide please go to http www beckmancoulter com hr contactus default asp 19 3 Warranty Subject to the exceptions and upon the conditions stated below Beckman Coulter warrants that this product shall be free from defects in workmanshi
43. 35 as acetone ey aa cores Baan bed 142 Changing the Tungsten Lamp 0 0 ccc ccc eee IR 142 Changing the deuterium lamp UV 0 0 0 cc een eee 143 Changing the Fuse 0 0 0 eee ees 144 Changing the FIERO sce ac occ oth juan Serie do arated oad deal EREMO RR 145 Section 16 Troubleshooting Power Up DIagmoSLl S u uie citm iter eid bc dag eiue ro abc ed 147 POE WICSSd0 CS sane teas apc 6 319 m dodi C oO ERU Mb dE Reta ea 148 Other Error Conditions sssssese RR RRRSMsnnhRRII 149 section 17 System Check Call System Check from the Main Menu 0 008 151 Instrument Information sss RR 151 Upgrading the Instrument Software 0 0 0 cece eee 152 Optical CNeCKS errana Cadets denos eod eee Ga eh oe a 152 Wavelength Check orks anxii tend atin a tg petet veu arenae ed oen en rei ten 153 MOIS OBEN eiu cars tases vss Lut LM E EE M M EE EE EE 154 Stav LIOM Seo WERE 154 ADSOLDADEe CHECK cess orari dedi rere dur epa oie e Ebr f pa eee SOS diee 155 PSV TT GIA Gi C P RR MEE 156 PEE Med O ERR E CO TET TT OO a 15 Facto SEVICE irato our dean dd deest estare hie are ee ote s tpa 157 section 18 Specifications Performance Specifications 0 00 RR 159 Physical and Environmental Specifications 000 159 Power and Other Specifications 2 0 0 0 cee eee 160 section 19 Replacement Parts Service Centers and Warranty Replacement Parts Sup
44. 73 16 where te Temperature in Fahrenheit tc Temperature in Celsius tk Temperature in Kelvin In the Tables screen 1 Touch the desired line to highlight it or touch Select by Number and enter the desired number 2 Touch OK to perform the function 3 Touch Cancel to return to the DNA Protein Tools screen NOTE Tables do not perform a function They simply provide information This function provides a table with a number of nucleotide translation conventions IUB GCG International Union of Biochemistry convention translates sequences for GENBANK University of Wisconsin Genetic Computing Group EMBL and the National Biomedical Research Foundation Staden The Staden convention is used by the Cambridge University database 115 DNA Protein Tools Mode Tables 116 Standard Genetic Code Amino Acid Codes and Masses DNA Protein Sizes DNA Sequence Triplets Decoder Sanger The Sanger convention is currently not used Stanford The Stanford convention is used by the Stanford University database This function provides the table of the standard genetic code This function provides a table with the names of the 20 common amino acids the single letter code the corresponding three letter abbreviation as well as its mass This function provides a table with conversion information for DNA and Proteins This function provides a table with the common amino acid names and its DNA Sequence Triple
45. CURES Dt et toten 116 Meme Pronos ssa iu aene i ta aki aa Ga eR en Su a SER 116 VI section 13 Carousel Sipper and Peltier Operation Carousel Holder 0 0 ccc ee eee ees 117 Fixed Wavelengths Measurements 0 0c cece eee eee 117 Wavelength SGdllis ian exire orb federa ie ide acd oe doe Ae oed moe bed died te 118 Ainsi mper 119 1 6 6151 08 6 0 0 gt os atrocem id aote Beet deseen diee ache rs ds 120 Fixed Wavelengths Measurements ssee RR 120 VWavelengttid dll susc rrn m Sete a end te at UET A a aed aad Reale teas 121 Ainsi cM 122 Peer MOdUIG Pm 123 PAWN EONS Soe asc tne oa e teres fn ce ence ee E T EE EEEE S 123 Section 14 Store Recall Send and Delete Data DIOLIRODUdEId cosces asa E aeea oss arta t aatis m md tende 125 storing Data Auto Manual lsssssese RR RR 125 single Reading MOU 2 014 sik sec in RE IG REGemxbepE Dee ra eek 125 Continuous Reading Mode sse RR III 126 storing Scans Wavelength Scan 0 0 cc ee e 126 Storing Kinetic Data Kinetics Time 0 0 0 0 ccc ee eens 127 Recalling Data Scans and Kinetic Runs 0000 127 FROCTITICIVBI EAs sateen atc ser dase eot ead diu Gaal Goer en ay aie cR et oats 127 Recalling Scans Wavelength Scan esessesee I 128 Recalling Kinetic Data Kinetics Time 0 0 ees 130 sending Data Scans and Kinetic Runs 00004 131 ScHUIHO alas t
46. ERR ok Touch OK to save your selections DU Series 700 User s Guide AT PN A24014 AA Fixed Wavelength Mode Parameter Setup Concentration Format Cancel Single Reading C Continuous Readings Cancel 48 To set the Concentration Format 1 Touch Concentration Format in the Options menu 2 Select the number of significant digits for the concentration results by touching the respective radio button 3 Touch OK to confirm To select the reading mode 1 Touch Reading Mode in the Options screen and choose one of these options e Reading Mode Single This feature is available for procedure readings to stop measurement reading fluctuations on the display once it reaches a stable reading This is the default setting Reading Mode Continuous This feature is only available by choosing one measuring wavelength NOTE With the continuous reading mode only the Blank button is displayed The Read button is not available since the readings are continuous and start automatically 2 Touch OK to confirm your selection After entering the analysis parameters you are ready to read the samples This description assumes that you have selected Single Reading default as the reading mode and that you are using a cell holder that holds one cell the Standard Cell Holder that comes with the instrument For instructions on using this function with a Carousel Cell Holder the Sipper Module or the Peltier T
47. History l vi 17 5 Lamp History The Lamp History provides the following information Lamp History VISIBLE The amount of time that the lamp has been on Hours Hours 90 4 e The number of times that the lamp has been turned on Cycles 72 Cycles e e The number of times that the instrument tried to turn the UV lamp on triggers Res Cycles 3 et Uv Triggers 7 After reviewing the lamp history Cancel OK e Touch Reset VIS to reset the Visible Lamp e Touch Reset UV to reset the UV Lamp e Touch OK to return to the System Checks screen 17 6 Factory Service The Factory Service requires a code Service Code NOTE These tests are not intended for customer use DU Series 700 User s Guide 157 PN A24014 AA System Check Factory Service 158 DU Series 700 User s Guide PN A24014 AA 18 1 Performance Specifications Operating Mode Source Lamp Wavelength Range Wavelength Accuracy Wavelength Resolution Wavelength Calibration Wavelength Selection Scanning Speed Spectral Bandwidth Photometric Readout Photometric Accuracy Photometric Linearity Stray Light Specifications Performance Specifications S Specifications NOTE Specifications are subject to change without notice Transmittance Absorbance and Concentration Tungsten visible and Deuterium UV 190 1100 nm 1 nm in Wavelength Range 200 900 nm Selectable 0 1 0 2 0 5 1 0 2 0 a
48. LI After you have entered the analysis parameters the samples are ready to be read Dye Incorporation Uw vis To enter the Dye Incorporation mode Fio Mncorporsuon cDNA un 1 Touch 96 Dye Incorporation in the Main Menu Reading Nucleatides pmoal Amount pmol 2 Inserta cuvette with a blank solution into the cell holder and Azsoo Assoc hasan Conc yM close the cell compartment to blank against air leave the Mass ug Blank cell position empty Pc NOTE If the lid of the cell compartment is open the instrument disables EET E E tae the Blank Read buttons a 3 Touch Blank to blank the instrument The screen displays the Options Blanking message in the bottom left corner of the screen Cancel 4 When the system has been blanked insert a sample cuvette into the cell holder and close the cell compartment 5 Touch Read to start the reading The screen displays the Reading message in the bottom left corner of the screen and then reports the results for the sample NOTE During the reading process the screen replaces the Read Blank buttons with a Cancel button You may touch Cancel to stop the reading and discard the data DU Series 700 User s Guide 101 PN A24014 AA Jo Dye Incorporation Analysis of Samples GT EDIDI HRPRUBUBIESNE NRANE On this results screen the 260 280 Ratio has been turned On and the ratio is reported together with Dye Incorporation results Cys Incorporation
49. Password Security pff Set Password Security List ee Cr mban Wew Password E dae we or on ss vo oe a s ow on v Cancel OK Instr Cr mban Password Security C off Set Password Security List OK 38 The Password screen enables you to set a password and a variety of security settings The security list enables you to control the accessibility of various functions For example you can prevent changing or deleting different stored programs without authorization To access the security settings 1 Touch Password in the Instrument Setup menu 2 Touch Set Password NOTE This enables you to assign a password required for the specified function You must assign a password before the screen activates the Security List option 3 Use the alphanumeric keypad to enter a new password 4 Touch OK to confirm the entry This activates the Security List 5 Touch Security List to lock various functions from unauthorized users DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 Instr eee a eo 6 Check the functions you want to control by touching each security List respective option 7 Touch OK to confirm the security options selected from the Security List New Program Edit Program 8 Enter the new password again to confirm Delete Program Update Software 9 Touch OK to return to the Instrument Setup menu NOTE Each time a us
50. RM 2031 or 930e The photometric accuracy is specified at 546 1 nm at 1 0A 1 Touch A to enter the wavelength 2 Enter the wavelength using the numeric keypad and confirm with OK NOTE The system must read 10 replicates of a blank and readings from the sample solution to calculate the results 3 Insert the appropriate cuvette and touch Blank and then Read This must be repeated 10 times The screen displays the results 4 Touch Cancel to return to the Optical Checks screen 155 System Check Optical Checks Drift Check The Drift Check lets you test the stability of the instrument Optic Mh al Drift Check 1 Touch A to enter the wavelength Wavelength 546 1 nm 2 Enter the wavelength using the numeric keypad and confirm with OK 3 Touch Start cancel Optic I7 Es n ndo This test takes a reading every minute for one hour Every Drift Check fifteen minutes the instrument uses linear regression to calculate the slope rate of change for the previous 15 minute interval Drift 0 b i paran er s The screen displays the last reading and slope for each 15 minute interval At the end of the hour the instrument calculates and displays the overall values Initial Reading 0 0001 Abs Final Reading 0 0032 Abs Dla mMin ea 4 Touch Cancel to return to the Optical Checks screen Last Abs 0 0012 Abs Cancel cH 156 DU Series 700 User s Guide PN A24014 AA System Check Lamp
51. Read to start the reading The screen displays the 0 2500 0 450 Reading message to the right of the concentration and 0 5000 0 956 adds the reading Net Abs to the line with the respective Seed concentration value NOTE Make sure you insert the standard cuvettes in the right sequence O7 MAR 2005 22 20 03 based on the entered concentration NOTE During the reading process the Read Blank buttons are replaced by a Cancel button You may touch Cancel to stop and discard the current reading 5 Continue until all standard cuvettes have been read and an absorbance value is associated with each concentration Bradford Bremer mm Alter reading the last standard the system calculates and displays Linear Curve the standard curve e Edit Stds goes to the Enter Concentrations screen The list in this screen now has absorbance values for each concentration You may edit information and or re read standards e Non Linear Linear Toggles between Linear and Non Linear curve fit By default the system applies the Linear curve fit e Force 0 Off On allows you to force the curve fit through Zero e a b c displays the coefficients of the standard curve The screen displays only one coefficient at a time Touch the button to see the next coefficient DU Series 700 User s Guide 15 PN A24014 AA Protein Assay Analysis Analyzing Samples 9 4 Analyzing Samples 16 OCT 2004 15 11 44 76 595 0 nm Dilution X 1 0000 T
52. S Nearest neighbor entropy R Gas constant 1 987 C Concentration from equation 11 in molar units pMol salt Millimolar salt concentration 1M user input Where the base identity 1s unspecified the calculations are performed using the average values for the pairs of nucleotides The higher the ratio of unspecified bases to the total bases the higher the uncertainty in the T calculation CRC Handbook of Biochemistry and Molecular Biology Nucleic Acids 1977 The value used for unspecified base is the average of the millimolar extinction coefficient for the four specified bases 3 The value used for unspecified base pair is the average of the millimolar extinction coefficient for all specified base pairs Rychlik W Spencer W J and Rhoads R E Nucleic Acids Research 18 6409 6412 1990 DU Series 700 User s Guide PN A24014 AA DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Calculations Breslauer K J Frank R Blocker H and Marky L A Proc Natl Acad Sci U S A 83 3746 3750 1986 6 The concentration factors provided in the literature generally agree that a factor of 50 should be used for double stranded DNA a factor of 33 should be used for single stranded DNA and a factor of 40 should be used for RNA when data are collected at 260 nm These factors are provided as default values However the user has the option of inputting any desired co
53. S 1 0000 shows the raw data absorbance values NIE ES e Dilution X lets you enter a dilution correction factor The displayed results are corrected for dilution using the following equation 09 FEB 2005 17 19 25 Con Conc x Dilution T Options e i lets you modify the default wavelengths and toggle background correction on and off When background correction is on you can modify the default background wavelength e Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings Options Touch More to go to the Options screen Concentration Path Length cm i Factor 50 000 1 0000 e Concentration Factor allows you to modify the default araia Mn zii i MB The default factor reported the referenced literature are dsDNA 50 ssDNA 33 RNA 40 e Concentration Format sets the number of significant digits Instrument Jis mU Setup for the calculated concentration e Path Length cm allows you to modify the default path length of 1 cm if you want to use small path length cells for very high sample concentrations e Store Data Off On lets you toggle the storage setting and manually store data e Save as User Program stores the selected parameters as a user program see User Programs on page 43 DU Series 700 User s Guide 85 PN A24014 AA Nucleic Acid Analysis Parameter Setup Oligo DNA Long and Oligo RNA L
54. Screw the grid back in place 6 Carefully stand the instrument upright 7 Plug the instrument in It is now ready for use again 146 DU Series 700 User s Guide PN A24014 AA 16 1 Power Up Diagnostics Troubleshooting Power Up Diagnostics l 6 Troubleshooting Each time you power up the instrument it performs a series of diagnostic tests automatically These include System Tests Memory Tests Voltage Tests A Calibration Lamp Tests Filter Adjustment The Self Check display lists these tests When each test completes successfully the screen adds a check mark after the test name If any of the tests do not finish successfully the screen displays an error message When the screen displays an error message take the recommended action that corresponds to the error message show in the following table see Error Messages on page 148 If any of the tests fail and the screen does not display an error message switch off the instrument then switch it on again DU Series 700 User s Guide PN A24014 AA 147 Troubleshooting Error Messages 16 2 Error Messages Table 16 1 Power Up Error Messages Error Message BEAM BLOCKED LAMP ALIGNMENT LAMP OUT LAMPS OVERHEATED LID OPEN MODULE REQUIRED OFFSET CORRECTION UV LAMP OUT VIS LAMP OUT 148 Recommended Action Remove whatever is blocking the beam in the sampling module and press the START soft key Replace the visible lamp see Chang
55. Setup Mode Peltier Module Temperature Control Instrument Setup If your instrument includes a Peltier Temperature Control Module T Operator ID Sample ID the Instrument Setup menu provides a Temperature Control eue EU option You can modify Temperature Modes using this menu Date amp Od Display amp Time Sound 1 Touch Temperature Control in the Instrument Setup menu to Lamp display the Temperature Control screen Lr USB Port Control Return Instr ret ote 2 Modify the desired parameters for the following options Temperature Control Temperature Wand Temperature Turns temperature control off or on and 37 C 2 C allows you to set the desired temperature p Idle 8 Hours Warning The warning alerts you when the actual temperature deviates from the set temperature You can turn the warning off or to on by entering the deviation from set temperature that triggers the warning Cancel Default Unit Select the temperature unit as Centigrade or Fahrenheit Idle The idle function causes the instrument to automatically turn temperature control off after the specified time Use this button to turn the idle function off or on by entering the amount of time in hours before the temperature control is automatically turned off NOTE As an alternative you can access the Temperature Control screen directly from the measurement mode by touching the Temperature Control icon at the bottom right of the
56. a teat ache ocean oe ae M Po eat Baan bee eae 131 sending Scan Data Wavelength Scan 0 0 cece eee eee 132 sending Kinetic Data Kinetics Time 0 0 0 ce eens 133 Deleting Data Scans and Kinetic Runs 0 0 0 0 0 ee 133 GIO TING ND Abela oe c ce ereina deea adn aut a oe Simin oiae Rean e Asai ee eeacease 133 Deleting Scan Data Wavelength Scan 0 0 ccc cee eee 135 Deleting Kinetic Data Kinetics Time 0 0 0 eee nes 135 Section 15 Maintenance Cleaning Requirements 0 0 0 ccc cee eee eee eee 137 SDOCITODROIONIGIBE cd curios Seat tos ee catcee Veet eee sasaeGe RIED 137 BISD e it Sach ches Gale ae de eee A O ne Ge Soh E E 137 Cell Cleaning Instructions slsese RR 137 SIBI MEER TERT has sats aera task eet den 197 Cell Cleaning Instructions leelsen RR RR 138 Gell DETCHOFATION a ciu asina ot dent d ee dne EL Rob m teta dae ic drum 139 Flowcell Maintenance Cleaning Instructions 0 0 0 0 ccc eee nne 139 Flowcell Cleaning Instructions lslsesee RR IIR 139 vii DU Series 700 User s Guide Conditioning a new Flowcell 0 0 0 ccc eee ee teens 140 Cleaning Procedure Daily 0 0 0 c ccc eee eens 140 Cleaning Procedure Contaminated Flowcells 00 0000 0 140 Cleaning Procedure Severely Contaminated Flowcells 0 141 Other information MERETRICIS 141 Dhaligind J dfiDS 235
57. ach calculation provides an equation followed by a reference number within parentheses Where applicable these reference numbers identify the equations described within other calculation descriptions NOTE The application uses the commonly used term extinction coefficient in place of the IUPAC term absorptivity These terms can be used interchangeably Background Correction and Net Absorbance Concentration Calculations DU Series 700 User s Guide PN A24014 AA It is possible to correct for raised baselines which may be caused by turbidity in the sample using background correction If you enable background correction the instrument subtracts the reading at the input wavelength from the reading at the analytical wavelength s to calculate a net absorbance reading Net Abs Absorbance Bkg Abs 1 where Absorbance Reading at the analytical wavelength Bkg Abs Reading at the background wavelength Only the calculated net absorbance may be displayed instead of all the raw absorbances If the background correction is disabled the net absorbance is equal to the reading at the analytical wavelength The 260 280 Ratio and the Single Ratio methods use the following equation to calculate the concentration Conc Net Abs x Conc Factor x Dil Factor 2 The Double Ratio amp Concentration dsDNA ssDNA and RNA methods use the following equation to calculate the concentration Conc Net Abs x Conc Factor x Dil
58. acil 9 9 dU Number of uracil bases user input Ex Average millimolar extinction coefficient of A C G U at 11 02 dN Number of unspecified bases user input Molar Extinction Coefficient Oligo RNA Short 94 For oligonucleotides shorter than 30 bases the base order affects the molar extinction coefficient to the extent that the simpler formula for long oligos does not provide an accurate determination To calculate the molar extinction for shorter oligos you must enter the sequence The system calculates the molar extinction coefficient Ea pc xyx at 260 nm in units of L umol cm using the equation ABC XYz 2 X ap gc exy eyz p ec ex ey x 103 9 where eag Millimolar extinction coefficient for each base pair c4 Millimolar extinction coefficient for each base DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Calculations Extinction Coefficient Oligo DNA RNA Long Short The extinction coefficient k at 260 nm in units of L umol cm 1s calculated from the molar extinction coefficient using the equation Koligo Eoligo x 10 Mol Weight 10 where oligo Molar extinction coefficient calculated using equation 6 7 8 or 9 Mol Weight Molecular weight of the oligo calculated using equation 4 or 5 Concentration Oligo DNA RNA Long Short The oligonucleotide concentration is calculated in both units of pM uL a
59. ains all the information needed to enable the instrument to be operated without any problems throughout its life span The manual is intended for use by the personnel who operate the instrument Accident and trouble free operation of the instrument can only be assured by adhering strictly to the instructions in the manual Such adherence results in less down time and lower repair costs and increases the lifesaving of the instrument This equipment complies with Class A limits for the FCC and EN 55011 requirements l Introduction Safety Precautions 1 2 Safety Precautions Electrical Safety Safety Against Risk of Fire Please read this entire manual before unpacking setting up or operating this instrument Pay particular attention to all danger and caution statements Failure to do so could result in serious injury to the operator or damage to the equipment Do not use or install this equipment in any manner other than what is specified in this manual Besides following the instructions in this manual users must comply with the general safety and accident prevention regulations of the country in which the instrument is used To reduce risks of electric shock this equipment is equipped with a three wire electrical cord and plug to connect the equipment to earth ground To preserve this safety feature Make sure the matching wall outlet receptacle is properly wired and earth grounded e Never use a three or two wire i
60. am A USB connectors for Printer Keyboard and or Memory Device 3 On Off switch pee 8 Plug in Power Supply DU Series 700 User s Guide PN A24014 AA System Description Design Beam Path The following schematic diagram shows the beam path of the Spectrophotometer Figure 2 4 Beam Path Halogen lamp LPT AN Lamp selection mirror KK Deuterium lamp a S Reference Mirror i rating el t f eiemen Splitter mirror Entrance slit ss Ss S p hn ss RS Pd Filter bos pa va Exit slit 4 BUTS 4 Mirror N M s Mirror S z N Cell compartment N DNE NEN Noy Monochromator Lens l Round cuvette compartment Measurement element 901604 ai DU Series 700 User s Guide PN A24014 AA System Description Unpacking the Instrument 2 3 2 4 10 Source Compartment A Unpacking the Instrument Operating Environment The source compartment is on the left side behind the display inside of the instrument It is provided with ventilation on the back side The lamp compartment contains the halogen and deuterium UV lamps A fan used for cooling the sample compartment and electric components is mounted on the back side The ventilation system operates automatically In general you should maintain a clear space of at least 15 cm 6 inches around the instrument for safety Good ventilation prevents the electro
61. assemble the Turbidity Cell Holder 1 Open the cell compartment 2 Insert the cell holder into the cell compartment in such a way that the locking screws on the holder are at the front 3 Take care to position the holder exactly The metal pins of the cell compartment should lock into the holder 4 Secure the front part of the holder with the two locking screws Figure 3 7 Installing the Turbidity Cell Holder 16 DU Series 700 User s Guide PN A24014 AA Multicell Holder Figure 3 8 Multicell Holder Top and Bottom DU Series 700 User s Guide PN A24014 AA Installation Cell Holders 3 The Multicell Holder can accommodate the following cuvette types e 10 20 and 50 mm rectangular cuvettes e 1 inch round cuvettes e inch rectangular cuvettes You can use only one cuvette type for a measurement On the top and bottom of the Multicell Holder are a variety of openings that accommodate different types of cuvettes Beside each opening is printed the type of cuvette for which it 1s intended 901602 ai EN 10 mm rectangular cuvette ES 20 mm rectangular cuvette EN 50 mm rectangular cuvette EN 1 inch round cuvette 1 inch rectangular cuvette Multicell Holder Installation To assemble the Multicell Holder 1 Open the cell compartment 2 Identify the correct opening for the selected cuvette type in the Multicell Holder 3 Insert the Multicell Holder in the cell compartment with the cell o
62. c Runs l 4 Deleting Scan Data Wavelength Scan To delete stored scan data from the Recall Data screen 1 Highlight the line with the Scan you want to delete 2 Touch Options 3 Touch Delete The instrument immediately deletes the scan data in the highlighted storage location Deleting Kinetic Data Kinetics Time To delete kinetic runs from the Recall Data screen 1 Highlight the line with the Run you want to delete 2 Touch Options 3 Touch Delete The instrument immediately deletes the kinetic data in the highlighted storage location DU Series 700 User s Guide 135 PN A24014 AA Store Recall Send and Delete Data Deleting Data Scans and Kinetic Runs 136 DU Series 700 User s Guide PN A24014 AA 15 1 Cleaning Requirements Spectrophotometer A Cell Cleaning Instructions DU Series 700 User s Guide PN A24014 AA Maintenance Cleaning Requirements 5 Maintenance Do not expose the instrument to extremes of temperature such as heating direct sunlight or other sources of heat All round unobstructed ventilation of the instrument must be assured at all times The instrument must not be operated or kept in extremely dusty damp or wet locations Keep the surface of the instrument the cell compartment and all accessories clean and dry at all times Splashes or spills on and in the instrument should be cleaned up immediately Clean the enclosure the cell compartment and all a
63. cal scan interval or resolution is 1 nm which is equal to a scan speed of 910 nm min 5 Touch OK to return to the scan mode DU Series 700 User s Guide 53 PN A24014 AA Wavelength Scan Mode Parameter Setup To set scale and units for the y axis Scale amp Units 1 Touch Options More and then Scale amp Units Units ane 2 Select Abs or T by touching the radio button Scale 3 Select Auto or Manual scaling Auto C Manual e With Auto scaling default the screen scales the scan 0 300 Abs 3 500 Abs to fit the graph area e With Manual scaling you can set the lower and upper limits of the y axis by touching the respective button and entering the appropriate value using the numeric keypad 4 Touch OK to return to the Options screen 5 Touch Return to return to the scan mode To toggle between the scan display graph and the tabulated scan data touch Select Table or Select Graph in the Options menu after taking a scan Wavelength Scan 351 0 0 647 Peak 0 615 353 0 0 584 0 576 Valley i 355 0 0 596 0 620 357 0 0 642 0 663 Peak 359 0 0 658 0 573 361 0 0 446 ih Return Options 54 DU Series 700 User s Guide PN A24014 AA 6 2 Scanning Wavelength Scan 450 Blanking Exit Cancel Options Wavelength Scan Reading Exit Options DU Series 700 User s Guide PN A24014 AA Wavelength Scan Mode Scanning 6 Before you can take a wavelength scan
64. can touch the UV Lamp icon on the measurement screen to change the actual setting As a standard feature the instrument has three ports located on the back wall of the instrument Figure 2 3 These ports enable you to output data and graphics to a printer They also let you connect a USB keyboard or a memory device USB 2 and 3 A Connectors These two USB ports let you connect a USB printer a keyboard a memory device or a device for memory cards These devices are controlled by the spectrophotometer 36 NOTE The printer must have a USB interface and must feature the Printer Command Language PCL Printers that use the Lightweight Imaging Device Interface Language LIDIL or are based on the Printing Performance Architecture PPA require Microsoft Windows and cannot be used with a DU Series 700 instrument DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 To view a list of devices connected to the ports Instr cee ots USB Port 1 Touch USB Port in the Instrument Setup menu The USB Port screen displays a list with information about the following connections Printer Not Connected Printer e USB Memory Keyboard NOTE This screen provides information only The instrument automatically detects connected devices 2 Touch OK to return to the Instrument Setup menu DU Series 700 User s Guide 37 PN A24014 AA Installation Instrument Setup Mode Password ee Cr mban
65. ccessories with a soft damp cloth A mild soap solution can also be used Dry the cleaned parts carefully with a soft cotton cloth Display Take care not to scratch the display Do not touch the screen with ball pens pencils or similar pointed objects Clean the display with a soft lint free oil free cotton cloth Diluted window cleaner liquid can also be used WARNING Under no circumstances should the instrument or the display or the accessories be cleaned with solvents such as white spirit acetone etc Cell Description Beckman Coulter cells for UV Visible spectrophotometers have two optical and two non optical facing sides The decal on one of the non optical surfaces identifies the type of material used for the optical windows A blue decal indicates silica windows which transmit in the UV and visible regions from 190 to 2500 nm A green decal indicates special optical glass windows which transmit in the visible region only from 320 to 2500 nm Always position the cell in the spectrophotometer so that the light is transmitted through the optical windows A higher than expected absorbance reading indicates that the cell may have been inserted in the wrong orientation 137 Maintenance Cleaning Requirements 138 Cell Cleaning Instructions 1 Rinse the cell with a mild solvent distilled water for aqueous solutions an organic solvent for organic materials as soon as possible after each use WARNING D
66. compartment see Figure 3 3 3 Take care to position the holder exactly The metal pins of the cell compartment should lock into the holder 4 Secure the front part of the holder with the two locking screws Figure 3 3 Installing the Standard Cell Holder 14 DU Series 700 User s Guide PN A24014 AA Installation Cell Holders 3 50 uL Single Cell Holder The 50 uL Single Cell Holder only accepts 50 uL Microcells from Beckman Coulter Inc Figure 3 4 50 pL Single Cell Holder 50 uL Single Cell Holder Installation To assemble the 50 uL Single Cell Holder 1 Open the cell compartment 2 Insert the cell holder into the cell compartment in such a way that the locking screws on the holder are at the front 3 Take care to position the holder exactly The metal pins of the cell compartment should lock into the holder 4 Secure the front part of the holder with the two locking screws Figure 3 5 Installing the 50 pL Single Cell Holder DU Series 700 User s Guide 15 PN A24014 AA Installation Cell Holders Turbidity Cell Holder The Turbidity Cell Holder is designed to give accurate quantitative measurements of light scatter in the DU Series 700 Spectrophotometer with conventional forward optics design Use this cell holder when you want to quantitate bacterial cultures or other turbid samples by absorbance measurements Figure 3 6 Turbidity Cell Holder Turbidity Cell Holder Installation To
67. ct a different language Each time you power up the instrument it performs a series of diagnostic tests automatically to ensure operation of major system components This procedure which takes approximately two minutes checks the system lamps wavelength calibration filter adjustment and voltage The display adds a check mark next to the test name to confirm its functionality When power up diagnostics are complete the Main Menu appears NOTE If any function does not pass or if any error messages appear during self check see Troubleshooting on page 147 2f Installation Main Menu 3 5 Main Menu lain Menu The Main Menu consists of two pages on the DU 730 From there 3 quo you can access common functions as well as all the available User Programs Fixed Wavelengt i applications modes Table 3 1 identifies each Main Menu soft key er and briefly describes the corresponding operation mode Wavelength Scan Kinetics Time Single Component protein A Pe e To display the second page of the Main Menu touch More Analysis F atein ASSa y Analysis System Instrument Checks Setup hain Wenu e To return to the first page touch Return Dye Incorporation DHA Protein Tools System Instrument Checks Setup Table 3 1 Main Menu Soft Key Options Soft Key User Programs Fixed Wavelength Wavelength Scan Kinetics Time Single Component Analysis SCA Protein Assay Analysis 28
68. cts firmly onto the new tungsten lamp 8 Insert the tungsten lamp into the lamp compartment Push the spring down 9 Check that the spring and the lamp socket are positioned correctly 10 Use a screwdriver to screw the back cover onto the instrument again 11 Plug in power supply again The Instrument is now ready for use Switch the instrument on 12 Reset the Lamp History see Lamp History on page 157 Changing the deuterium lamp UV DU Series 700 User s Guide PN A24014 AA A 1 Switch the instrument off 2 Unplug the power cord WARNING The instrument must remain switched off until you have finished changing the lamp WARNING Wait until the lamp has cooled 3 Use a screwdriver to remove the cover from the back of the instrument the screws may be slotted or cross headed 4 Place the cover and the attached fan carefully beside the instrument take special care with the fan cable 5 Unplug the deuterium lamp 4 Cat No A23792 from the socket by pushing down on the safety contact 6 Use a screwdriver to unscrew the two fastening screws 3 the screws may be slotted or cross headed out of the socket 7 Holding the lamp socket lift the deuterium lamp up out of the lamp compartment remove the complete unit including the cable 143 Maintenance Changing the Fuse 15 3 Changing the Fuse 144 8 Carefully insert the new deuterium lamp into the lamp compartment WARNING Do no
69. destination s by touching the respective radio button 3 Touch OK to send the data NOTE The number in brackets shows the total number of data assigned to this selection The instrument automatically sends the data as a single DATALOG file to the memory device using the CSV Comma Separated Value file format The file name uses the following format DLYear_Month_Day_Hour_Minute_Second csv NOTE CSV files are the preferred format for data import into spreadsheet and graphing programs as well as statistical packages DU Series 700 User s Guide 131 PN A24014 AA Store Recall Send and Delete Data Sending Data Scans and Kinetic Runs Sending Scan Data Wavelength Scan Options Scale amp Units Ce e Return 2f OlT Oe4 Scan 1 2ZU OCT 04 Scan 2 l1 Mo 4 Scan 3 11 MOVv 04 Scan 4 Return 132 quen Es pns E 423 453 nm A 5 0 nm 16 54 00 423 453 nm A 5 0 nm Tes 4235 4535 nm 40 5 nm 14 10 47 423 453 nm A 5 0 nm Instrument Setup Wavelength Scan wr Options You can send scan data to a printer or a memory device using the available USB ports Since the system automatically senses connected devices it sends the data to all available devices To send scan data directly from the Wavelength Scan mode Touch Options Touch More Touch Send Data USB Port icon The instrument immediately sends to the connected devices the data of all scans that currently reside in me
70. e UV lamp is ready When finished reading the sample the instrument displays the result Absorbance Reading or Calculated Concentration NOTE For instructions on using a Carousel Cell Holder a Sipper or a Peltier Temperature Controller see Carousel Sipper and Peltier Operation on page 117 NOTE For instructions on printing and storing data see Store Recall send and Delete Data on page 125 DU Series 700 User s Guide 49 PN A24014 AA Fixed Wavelength Mode Parameter Setup 50 DU Series 700 User s Guide PN A24014 AA Wavelength Scan Mode Parameter Setup 6 Wavelength Scan Mode The Wavelength Scan mode shows how light is absorbed by a solution over a given wavelength range You can display wavelength scans in either Absorbance Abs or Transmittance Vo T The scans can be scaled manually and automatically This mode lets you determine peaks and valleys and zoom into areas to see more details You can obtain the absorbance or transmittance values at a given wavelength by moving the cursor to any point on the x axis of the graph Track function You can also tabulate the scan data When recalling a stored scan you can overlay this reference scan with the current scans 6 1 Parameter Setup Wavelength Scan VIS To enter the Wavelength Scan mode 1 Touch Wavelength Scan in the Main Menu 2 Touch Options for Parameter Setup Reference ff O More displays further options in the Options screen
71. e purge is set up for a manual start the instrument waits for you to touch Purge e In the automatic mode the purge begins immediately after the reading without operator intervention At this time if the sample is going to waste you can place a demineralized water purge at the sample inlet to rinse the sample cell between readings Leave the inlet tube in the purge solution until the Sipper pump Stops The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date NOTE If you need to stop the purge cycle during the purge interval touch Cancel When the sample purge is complete the instrument is ready for the next sample DU Series 700 User s Guide PN A24014 AA Carousel Sipper and Peltier Operation Peltier Module l 3 13 3 Peltier Module For information on changing sample modules loading and inserting the Peltier Temperature Control Module or setting the temperature parameters see Peltier Temperature Control Module on page 25 All Modes Kinetics Time VISX 570nm With the Peltier Temperature Control module installed the instrument behaves just like a system with a regular Single Cell Holder However with the module installed a Thermometer Icon and the current temperature appears at the bottom right corner of the screen You may touch the Thermometer Icon see arrow to change the Peltier Settings in an instant without returning to the Instrument
72. e running an assay that is not available as a method Units allows you to select the desired concentration unit and or define new units Concentration Format lets you determine the number significant digits for the concentration values Save as User Program stores the selected parameters as a user program see Store Recall Send and Delete Data on page 125 DU Series 700 User s Guide 1 1 PN A24014 AA Protein Assay Analysis Parameter Setup Stan zal fhann eo ee os Wavelength Options Stan s Pee eee Cb Units mg mL Bradford 595 0 nm Enter Concentration mg mL Met 0 5000 Edit Delete Delete Conc Line Abs Done Cancel 72 Touch on the Standard Curve Setup screen to display the Wavelength Options screen 4 displays the current wavelength To change it touch 4 and enter the desired wavelength using the numeric keypad e BKG Corr toggles background correction between on and off When active you can set the background wavelength by touching the BKG button NOTE With background correction active the analysis subtracts the absorbance reading at the background wavelength Abspy from the absorbance reading at the analytical wavelength Abs The system reports the net absorbance readings Absg and uses them for all calculations AbSnet Ab ADSpk To change the unit touch Units in the Standard Curve Setup screen e To select an existing unit touch
73. ed power cord into the connector on the back of the instrument and a main socket 100 120 V 200 240 V 50 60 Hz NOTE The unit is shipped with a UL CSA approved 115 Vac power cord with a NEMA 5 15P style plug North America or a 230 Vac harmonized power code with a continental European plug e Use only earthed sockets e Check the power cable for damage before use DU Series 700 User s Guide 1 1 PN A24014 AA System Description Power Up Applying Power 12 DU Series 700 User s Guide PN A24014 AA 3 1 Cell Compartment Figure 3 1 Cell Compartment 3 2 Cell Holders Standard Cell Holder DU Series 700 User s Guide PN A24014 AA Installation Cell Compartment Installation The spectrophotometer has been designed in accordance with the current state of the technology and offers a choice of different modules and interchangeable cell holders for specific applications To prevent external light from interfering with the measurement the cell compartment has a light proof cover NOTE Close the cover before taking a measurement The DU Series 700 Spectrophotometer comes equipped with a Single Cell Holder which is the Standard Holder It holds one standard 1 cm rectangular cuvette 13 3 Installation Cell Holders Figure 3 2 Standard Cell Holder Standard Cell Holder Installation To assemble the Standard Cell Holder 1 Open the cell compartment 2 Insert the cell holder into the cell
74. ee 34 LDC ONO Doer otratecetee ts E ardor th recdon d ame decima egg aoe tee eis ake 34 UO ONL seat cee Ceah Geos bea ea ate ceca 2 ane tl chaian ees ok ane ata A EE 36 PAGCWONG wien tee Ka nasi e Dek oa Raa a ERE h eee hae EGEE 38 Carousel and Module Options 0 0 0 ccc eee eee 40 tcl L sUB 40 SPPE MOUE cit uta mti Ath creed dua dos abore etes recie hib tact eer aras uE 41 Peltier Module Temperature Control 0 0 0 0 cece eee 42 section 4 User Programs storing a User Program sssssesse RR RR RR RR 43 Recalling a User Program ee RR 44 Deleting a Stored User Program isissssses B 44 sectionb Fixed Wavelength Mode Parameter SB oososcd ea tatu tu dedu EE POP LESS eI 45 section 6 Wavelength Scan Mode Parameter Set seeds meii erede ie Iicnerau bee qp SEES 51 Ie EDISON TM 55 Section 7 Kinetic Time Mode Parameter Sel a naanduetde ce ben oen pw E eq ene E PER Qus Gees 5 Taking the Kinetics Readings 0 0 ccc cee eee eee 58 Analysis or a Kinetic RUN wads ccn bre Ec oe ede eds ote ee ede 59 section8 Single Component Analysis Mode SCA Parameter Setup 0 RR RR IRR IRR IR Ran Standard CUVE SUD 6 528 dtu dI RAE Ehe RE o RES cae ARS C OBITIGIETIES SEUD coord ditat urbe Sex o Br Y eh e Neo i Ce e eb cus Redding LAIR OS sss cicuckoa rece Pt een ners DR ede Patito mo etna Analyzing Samples sssssesse
75. eee ees section 9 Protein Assay Analysis Method Description z uude nicks ra Er ERE aa DOG OU sata m due Russcedhuara discors d awtedctns dad daiedion d poteet eet tt Sois e aha EUIS EBORE BIUEBI a ae ENRE bd Node est Mar dc d EROR d LIN Oe seas ect crest aac ah i eg Sak MM GONOMGGOIG te hpucaartor nok Goa Eo RIP ur bre A ede 8 ad eR aea ER eee NUR Bicinchoninate BCA n nnana cc eee RR IR Paramotor SB Sexes oak tenui sient Sate aah ere eth ok a ass aoe haat LE ae Standard Curve Setup aute bidon deret putabo et Dao pdt aba Bernier Reading Standards llssessee RR Analyzing Samples ssssssesses RR RR RI Section 10 Nucleic Acid Analysis Method Description 0 0 00 c Rn MM M RR III Zur E CPCPE S AE eT onde oe Aedes rath eae re ea ee eee eee De Double Ratio amp Concentration x uenit nica uc ok Wee t eu ek et e dsDNA ssDNA and RNA Peach x T SN ebd ae ERE bt ced Oligo DNA Long and Oligo RNA Long sssssenn nn RR Oligo DNA Short and Oligo RNA Short ssssssser ee Parameter SetllD ice casa cest eter aep uadeqekds arem probes 260 280 Ratlo and Single Patio i no to ete e breit bees Double Ratio amp Concentration lsslseeen RR dsDNA ssDNA and RNA 0 0 eee eee Ie Oligo DNA Long and Oligo RNA Long 0 0 0 eee Oligo DNA Short and Oligo RNA Short
76. emperature Control Module see Carousel Sipper and Peltier Operation on page 117 Before taking measurements you need to blank the instrument on air no cuvette in the light path or by using a cuvette with a blank solution which is recommended for best results DU Series 700 User s Guide PN A24014 AA Fixed Wavelength Mode Parameter Setup 5 NOTE Read is disabled until the blank reading is taken 1 Insert the blank cuvette into the cell holder and close the cell Fixed Wavelength VIS 9 650 nm compartment Q Q Q Q abe 2 Touch Blank to take the blank reading When done the instrument enables the Read button as pie 3 Insert a sample cuvette into the cell holder and close the cell compartment 07 MAR 2005 19 33 54 NOTE If the lid of the cell compartment is open the instrument disables the Blank and Read buttons 4 Touch Read to take the sample reading FN Optians When trying to read a Blank or a Sample the appropriate source must be turned on The system assures that this is the case You may observe the following e The UV lamp automatically turns on after you have entered a wavelength in the UV spectrum In this case you have to wait for the UV lamp to warm up before you can take readings During the warm up phase of the UV lamp the screen displays a Warming up message and flashes the UV lamp symbol When the UV lamp is turned on automatically the instrument performs the reading as soon as th
77. end and Delete Data on page 125 OFY MAR 2005 22 22 50 FN Optians DU Series 700 User s Guide TH PN A24014 AA Protein Assay Analysis Analyzing Samples 78 DU Series 700 User s Guide PN A24014 AA 10 1 Method Description 260 280 Ratio Single Ratio Double Ratio amp Concentration dsDNA ssDNA and RNA DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Method Description Nucleic Acid Analysis The Nucleic Acid Analysis mode provides methods for DNA RNA and oligonucleotide analysis including the calculation of absorbance ratios and concentrations Some of the methods also determine molecular weight nucleotide length extinction coefficient concentration and theoretical melting temperature NOTE When calculating a concentration from 2 default is 260 nm the wavelength should not be changed according to text books and articles on the subject NOTE All methods in this mode require the UV lamp You may switch it on manually and let it warm up sufficiently for best results If not turned on the instrument turns the lamp on automatically before taking the blank measurement using the minimum warm up time The UV Lamp icon appears in the display The 260 280 Ratio method allows you to calculate a 260 280 absorbance ratio with optional background correction at 320 nm The Single Ratio method allows you to calculate an absorbance ratio using any two wavelengths of choice with an optio
78. ent Setup menu Cancel OK DU Series 700 User s Guide 33 PN A24014 AA Installation Instrument Setup Mode Display and Sound Preferences Instr emn mant ee T Display Sound Display Contrast W Reading done Timer Short Long pem dom 34 Lamp Control Use the Display amp Sound screen to set the audiovisual preferences 1 Touch Display amp Sound in the Instrument Setup menu The screen displays four options e Display Contrast lets you adjust the display contrast to suit lighting conditions and viewing angle e Screen touch The instrument default is off To make a short beep every time by touching the screen activate the Screen touch option e Reading done The instrument default is set to make a short beep every time a reading is complete To turn off the Reading done sound deactivate the Reading done option e Timer lets you change the length of the timer sound touch Short or Long Long beeps are better for noisy environments 2 Touch OK to confirm The screen returns to the Instrument setup menu The halogen gas filled tungsten lamp produces light in the visible spectrum 320 to 1100 nm The deuterium lamp UV lamp produces light in the ultraviolet spectrum 190 to 360 nm In the overlap zone from 320 to 360 nm you can use either the deuterium lamp UV lamp or the halogen lamp for measurements The lifetime of the lamps is influenced by on off operation and the le
79. enter the coefficients of a mg mL 0 01 known standard curve p pul son e A lets you enter the wavelength and turn background User Program correction off default or on e Units allows you to select the desired concentration unit and or define new units Instrument e Concentration Format lets you determine the number of Return Setup RM fo significant digits for the concentration values e Save as User Program stores the selected parameters as a user program see Store Recall Send and Delete Data on page 125 The Define Coefficients screen allows you to select the curve fit Cuel 7 Define Coefficients and enter the known coefficients a and b for a linear fit and a b PA and c for a non linear quadratic fit To use this screen T incar cortar 1 Touch Linear Non Linear and select the desired curve fit equation Te PSA e e 2 Touch each of the enabled buttons a b c and enter the respective coefficient using the numeric keyboard 3 Touch Done when the setup is complete ancel A standard curve is now available and you can measure unknown samples and calculate the concentrations 64 DU Series 700 User s Guide PN A24014 AA Single Component Analysis Mode SCA Reading Standards S 8 2 Reading Standards SCA VIS 600 0 nm After you have entered the concentrations for the standards the Read Standards system is ready to read the standard cuvettes mg mL Met 1 Inserta cuvette w
80. er attempts to perform one of the locked functions an alphanumeric keypad opens in which the user must enter the password before using those locked functions I t ET M TT Cte T Io deactivate a password 1 Touch Password in the Instrument Setup menu 2 Use the alphanumeric keypad to enter the former password and confirm with OK STU Cancel i Instr ena aen 3 Touch Set Password This opens the alphanumeric keypad Password Security C off Set Password Security List OK DU Series 700 User s Guide 39 PN A24014 AA Installation Instrument Setup Mode Instr Cr mban New Password E ae ac or on ee EXESESESES opman Cancel Carousel and Module Options Instrument Setup Operator ID Sample ID lt Off gt lt Off gt Date amp Display amp Time Sound Lamp Carousel List to ee z Carousel Options Blank 1 Read 1 7 Blank 1 7 Read 1 7 Blank 1 Read 2 7 Blank 1 3 5 Read 2 4 6 Cancel aia E K 40 4 On the alphanumeric keypad leave the New Password field blank and touch OK This deactivates the former password and returns to the Password screen NOTE Use this function to delete the former password or to enter a new one Carousel If your instrument includes a Carousel Holder the Instrument Setup menu includes Carousel Options You can activate the Carousel Holder and modify the carousel parameters using in this menu 1 Activate the Carousel Holder
81. eries 700 User s Guide PN A24014 AA DNA Protein Tools Mode Calculations l 2 To enter the mode Calculations Protein Conc from Amina Acid Sequence 1 Touch Protein Concentration in the Calculations menu 2 Touch Info to display the available information for this Protein Concentration mg ml 0 0397 function Molar Exineroncecmeen 00380 3 Touch Calculate to perform the calculation and display the Protein Extinction Coefficient 0 3919 result s based on the parameters set in Options Calculate Options Options Touch Options to set the parameters for the calculation of Tyrosines Mole Weight 14 39338 5 Touch the parameter that identifies the value you want to aE nero hane Absi280nm change and set a parameter either by 16 0 1000 5 as eed 2 1 0000 selecting the radio button that displays the desired value NOTE The Preference button allows you to choose the factor for Cysteine which is 60 or Cystine which is 120 Preference Cysteine 170 DU Series 700 User s Guide 105 PN A24014 AA DNA Protein Tools Mode Calculations Radioactive Decay Correction 106 When working with radiolabeled DNA probes or other radiolabeled assays you may need to correct for the radioactive decay This function of the DNA Protein Tools performs a half life correction for the radioactive substance used in the assay or experiment The following parameters must be supplied e Original Date e Orig
82. es to the Enter Concentrations screen The list in this screen now has absorbance values for each concentration You may edit information and or re read standards e Non Linear Linear toggles between Linear and Non Linear curve fit By default the system applies the Linear curve fit 0 1500 mug mL Curve Fit 0 9995 War 0 0005 Thee e Force 0 Off On allows you to force the curve fit through Linear Zero e a b c displays the coefficients of the standard curve The screen displays only one coefficient at a time Touch the button to see the next coefficient The bottom of the screen displays the r value correlation coefficient for this standard curve together with the variance Var This allows you to judge the quality of the curve fit Try different parameters such as Force 0 and or Linear or Non Linear curve fit to see if the quality of the curve fit can be improved When you are satisfied with your standard curve touch Done to store the coefficients and to start analyzing your samples 66 DU Series 700 User s Guide PN A24014 AA Single Component Analysis Mode SCA Analyzing Samples S 8 3 Analyzing Samples NOTE If the Read button is grayed out you need to blank the system before you can read samples 600 0 nm 1 Insert a sample cuvette into the cell holder and close the cell compartment 2 Touch Read to read the sample The screen displays the result Eton e with the corresponding unit al Opt
83. eteriorated Fill all the cells with the same solution and verify that the readings are sufficiently similar before recording sample results For a complete description of the Beckman cell line refer to the Supplies and Consumables Catalog Bulletin 8500A In the United States call 800 742 2345 Outside the United States contact the local Beckman office Flowcell Maintenance Cleaning Instructions DU Series 700 User s Guide PN A24014 AA Flowcell Cleaning Instructions Flowcells exhibit unique cleaning problems due to the difficulty in cleaning the interior surfaces Experience has shown that most problems with Flowcells are due to the cells not being clean Dirty cells cause air bubbles to be entrapped may cause errors due to reduced transmission and may contaminate the sample It is important that samples and cleaning agents not be left in a Flowcell for long periods of time When not in use the cell should be flushed and filled with distilled or deionized water If this is not done substances will be deposited on the interior surfaces which may be very difficult to remove Also a Flowcell should never be allowed to air dry It should either be kept filled with distilled water or dried with pure bottled air or dry nitrogen 139 Maintenance Cleaning Requirements 140 Use only spectral grade alcohol and pure distilled or deionized water when cleaning or flushing Flowcells Solutions may be recycled during cleaning proced
84. g x dG MWy x dy MWy x dN 18 02 5 where MW Molecular weight of adenine 329 2 g mol dA Number of adenine bases user input MWc Molecular weight of cytosine 305 2 g mol dC Number of cytosine bases user input MWg Molecular weight of guanine 345 2 g mol dG Number of guanine bases user input MWy Molecular weight of uracil 306 2 g mol DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Calculations dU Number of uracil bases user input MW Average molecular weight of A C G U at 321 45 g mol dN Number of unspecified bases user input Molar Extinction Coefficient Oligo DNA Long For oligonucleotides longer than 30 bases if the number of each type of base is known the molar extinction coefficient oiigo at 260 nm in units of L umol em is calculated using the equation oligo ea X dA zc x dC eg x dG er x dT ey x dN x 1073 6 where c4 MMillimolar extinction coefficient of adenine 15 4 dA Number of adenine bases user input cc Millimolar extinction coefficient of cytosine 7 4 dC Number of cytosine bases user input eg Millimolar extinction coefficient of guanine 11 5 dG Number of guanine bases user input ep Millimolar extinction coefficient of thymine 8 7 dT Number of thymine bases user input en Average millimolar extinction coefficient of A C G Tat 10 75 dN Number of unspecified bases
85. gth of the protein One of the following parameters must be supplied e DNA Size in bases Converts to Protein Size Converts to Protein Length or Protein Size in kDa Converts to DNA Size Converts to Protein Length e Protein Length in Amino Acids Converts to DNA Size Converts to Protein Size Equation dnaprot input x 3 protgna input x 3 protgna input x 0 11 where dnagize Size of DNA bases protgjze Size of Protein kDa Protiength Length of Protein amino acids To encode Amino Acids divide the size of the DNA in bases by 3 To calculate the size of the DNA multiply the number of amino acids by 3 The predicted size of the protein is the number of amino acids times 0 11 kDa 0 11 kDa is the average molecular weight of an amino acid 114 DU Series 700 User s Guide PN A24014 AA Temperature Conversion 12 3 Tables Tables Nucleotide Naming Conventions Standard Generic Code 1 2 Cancel Select by Number Nucleotide Naming Conventions DU Series 700 User s Guide PN A24014 AA DNA Protein Tools Mode Tables 2 This function provides temperature conversions The following parameters must be supplied e Temperature in Fahrenheit Celsius or Kelvin Converts to Fahrenheit Celsius or Kelvin Equation tc 0 55556 x tf 32 te 1 8 x tc 32 tk 0 55556 x te 32 273 16 te 1 8 x tk 273 16 32 ik tc 2 3 16 te tk 2
86. gth to Cy3 550nm or Cy5 650 nm DNA Protein Tools The DNA Protein Tools mode does not take measurements The mode provides a number of calculations conversations and tables to aid you in common daily tasks System Checks The System Checks mode lets you check the performance of the instrument photometric accuracy photometric noise stray light wavelength accuracy lamp history and printer check Recall Data The Recall Data mode lets you store recall send and erase data from the Datalog Instrument Setup The Instrument Setup mode allows you to configure the instrument and the module based on your specific requirements DU Series 700 User s Guide 29 PN A24014 AA Installation Alphanumeric Keypad 3 6 Alphanumeric Keypad Instr mamat Cheba ee Sample ID a um c S Operator ID dae wc o on e n p nnn Gancel K 30 Each time an operation requires input the alphanumeric keypad opens Use this screen to enter letters numbers and symbols as needed when programming the instrument Unavailable options are grayed out indicating that those functions do not apply to your operation mode The icons to the left of the screen allow you to choose an entry mode e ABC alphabetic When entering alphabetic characters such as user entered units this key allows you to toggle between upper and lower case letters It is inactive on some screens e symbols Lets you enter punctuation symbols and nu
87. h a length of more than 30 bases In this method the calculation of the Theoretical Melting Point Tm for DNA can be far from the true value when the oligo is very short Oligo DNA Short and Oligo RNA Short These two methods allow you to calculate the purity absorptivity extinction coefficient concentration and melting temperature DNA only based on the base sequence and the absorbance at 260 nm Short nucleotides are typically between 10 and 30 bases The maximum allowable value is 40 bases For equations see Calculations on page 91 The methods use 260 and 280 nm analytical wavelengths and 320 nm as the optional wavelength for background correction You can change the second analytical wavelength A and the background wavelength The analytical wavelength of 260 nm is used to determine the concentration and cannot be changed NOTE Short oligonucleotides are considered those with a length of less than 30 bases The Oligo DNA Short and Oligo RNA Short methods apply the nearest neighbor algorithm for best results DNA Breslauer K J Frank R Bl cker H Marky L A Proc Natl Acad Sci USA 83 3746 3750 1986 RNA Freier S M Kierzek R Jaeger J A Sugimoto N Caruthers M H Neilson T Turner D H Proc Natl Acad Sci 83 9373 9377 1986 80 DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Parameter Setup l 0 10 2 Parameter Setup Nucleic Acid Analysis To enter the N
88. h the button you want to change day month or year ul 2 Use the up and down arrows to select the desired value a 3 Touch OK a Cancel OK DU Series 700 User s Guide 107 PN A24014 AA DNA Protein Tools Mode Conversions 12 2 Conversions Conversions 1 ug of dsDMA to pmol pmol of dsON4 to pg and ng ra 0 Cancel Select by Number Temperature Conyers i Information ng DNA In the Conversions screen 1 Touch the desired line to highlight it or touch Select by Number and enter the desired number 2 Touch OK to perform the function 3 Touch Cancel to return to the DNA Protein Tools screen NOTE When entering a function the instrument may display a result screen without values When this happens touch Options first and enter or change the parameters before you touch Calculate to calculate and display the result s Most functions provide additional information such as references or calculation descriptions When extra information 1s available the Info button 1s enabled To anne EINES EE E access this information touch Info ug 10 3pg N M is the number of nucleotides The average molecular weight of nucleotides is 660 pg pmoal Micrograms or dsDNA to Picomoles This function converts the amount of dsDNA ug to pmol The following parameters must be supplied e Length of DNA in base pairs e Amount of dsDNA in ug Equation DNApmot DNA g x pmol 660pg
89. hat is currently in use confirm whether you want to replace it Cancal OK rU DU Series 700 User s Guide 43 PN A24014 AA User Programs Recalling a User Program Fixed Wavelength gqug Fixed LUE k velen gth Select by Delete Cancel Number Program 4 3 Deleting a Stored User Program Delete Program Program 988 SCA Delete Program Se 44 In the Program Name screen enter a Program Name with up to 28 characters NOTE The alphanumeric keypad appears with a default name name of the mode for the user program You can use the keypad to change the name or enter a different name 5 Touch OK to save the program parameters under the chosen name and return to the operating mode To recall a previously stored user program Touch User Programs in the Main Menu to display all available user programs Select the user program touch the respective line and highlight the program or touch Select by Number and enter the User Program Number then touch OK Touch Start to run the program To delete a previously stored user program Touch User Programs in the Main Menu to display a list of all user programs Select the user program touch the respective line and highlight the program or touch Select by Number and enter the User Program Number then touch OK Touch Delete Program Touch OK to confirm deletion DU Series 700 User s Guide PN A24014 AA 5 1 Parameter Setup Fixed Wa
90. he bottom of the screen displays the r value correlation coefficient for this standard curve together with the variance Var This allows you to judge the quality of the curve fit Try different parameters such as Force 0 and or Linear or Non Linear curve fit to see if the quality of the curve fit can be improved When you are satisfied with your standard curve touch Done to store the coefficients and to start analyzing your samples NOTE If the Read button is grayed out you need to blank the system before you can read samples 1 Insert a sample cuvette into the cell holder and close the cell compartment 2 Touch Read to read the sample The screen displays the result with the corresponding unit NOTE During the reading process the Read Blank buttons are replaced by a Cancel button You may touch Cancel to stop and discard the current reading 3 Touch Options to access parameters for the sample readings e More provides more parameters in the Options screen e Dilution X lets you enter a dilution correction factor for the samples The displayed results are corrected for dilution using the following equation Con Conc x Dilution Timer Icon sets the timer Using the timer does not affect the readings that the instrument 1s taking The times are not stored with sample readings DU Series 700 User s Guide PN A24014 AA Protein Assay Analysis Analyzing Samples O Options 4 Touch More to go to the Op
91. hock disconnect the instrument from the power source before servicing the lamps To prevent a possible burn allow the lamp s to cool at least 30 minutes before handling The UV lamp generates UV light Do not look directly at an operating lamp without wearing UV protective eye glasses Use of Hazard Information The following symbols appear in the manual WARNING Users must comply with this warning for their own safety Failure to do so may result in an injury WARNING This symbol if noted on the instrument indicates a hot surface NOTE A note contains important information which users must take into account when handling the instrument Precautionary Labels Read all labels and tags attached to the instrument Personal injury or damage to the instrument could occur if not observed This symbol if noted on the instrument refers to the instruction A manual for operational and or safety information DU Series 700 User s Guide 3 PN A24014 AA Introduction Safety Precautions Waste Management and Recycling This symbol is required in accordance with the Waste Electrical and Electronic Equipment WEEE Directive of the European Union The presence of this marking on the product indicates that the device A28219 AA pee xj es EPS was put on the European Market after August 13 2005 and 2 must not be discarded using the municipal waste collection system of any member state of the European Union Custome
92. ians NOTE During the reading process the Read Blank buttons are replaced by a Cancel button You may touch Cancel to stop and discard the current reading Jl CT UUS 08 57 12 3 Touch Options to access parameters for the sample readings More provides more parameters in the Options screen e Dilution X lets you enter a dilution correction factor for the samples The displayed results are corrected for dilution using the following equation Con Conc x Dilution COIT e Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings Options 4 Touch More to go to the Options screen of Sample C Limit I Replicates 1 Off e of Sample Replicates lets you enter the number of Senden sample replicates 1 to 3 Standard Curve Off NOTE When analyzing two replicates the instrument calculates the c Save as average When analyzing three replicates the instrument calculates the Potro guam mean and the coefficient of variation CV if enabled e CV Limit Off On If three replicates are selected the button CV Limits will be enabled and you can toggle the reporting of the Coefficient of Variation CV limit on or off and set a CV limit Samples that are outside of the specified CV limit are flagged with OUT e Standard Curve allows you to the Standard Curve Setup parameters Instrument 5etup Return NOTE Y
93. if required by Beckman Coulter be returned to the factory transportation charges prepaid and will be returned to Buyer with transportation charges collect unless the product is found to be defective in which case Beckman Coulter will pay all transportation charges d Beckman Coulter shall be released from all obligations under all warranties either expressed or implied if any product covered hereby is repaired or modified by persons other than its own authorized service personnel unless such repair by others is made with the written consent of Beckman Coulter IT IS EXPRESSLY AGREED THAT THE ABOVE WARRANTY SHALL BE IN LIEU OF ALL WARRANTIES OF FITNESS AND OF THE WARRANTY OF MERCHANTABILITY AND THAT BECKMAN SHALL HAVE NO LIABILITY FOR SPECIAL OR CONSEQUENTIAL DAMAGES OF ANY KIND OR FROM ANY CAUSE WHATSOEVER ARISING OUT OF THE MANUFACTURE USE SALE HANDLING REPAIR MAINTENANCE OR REPLACEMENT OF THIS PRODUCT Representations and warranties made by any person including dealers and representatives of Beckman Coulter which are inconsistent or in conflict with the terms of this warranty shall not be binding upon Beckman Coulter unless reduced to writing and approved by an expressly authorized officer of Beckman Coulter DU Series 700 User s Guide PN A24014 AA
94. ils see Standard Curve Setup on page 61 Touch Coefficients if you want to enter the coefficients from a previous standard curve For details see Coefficients Setup on page 64 Standard MEE Coefficients Cancel Standard Curve Setup Standard Curve Setup Use the Standard Curve Setup screen to set the parameters Standards A Setup Standards Setup allows you to enter the concentrations for TP F each standard This also determines the number of data nits Concentration Format f mg mL 0 01 points you will have for the standard curve 5 7 TET sarang lets you enter the wavelength and turn background correction off default or on Units allows you to select the desired concentration unit and or define new units Instrument Setup Return Concentration Format lets you determine the number significant digits for the concentration values Save as User Program stores the selected parameters as a user program see Store Recall Send and Delete Data on page 125 DU Series 700 User s Guide 61 PN A24014 AA Single Component Analysis Mode SCA Parameter Setup tands Daten Touch on the Standard Curve Setup screen to display the wavelength Options Wavelength Options screen e a displays the current wavelength To change it touch A and enter the desired wavelength using the numeric keypad e BKG Corr toggles background correction between on and off When active you ca
95. inal Activity in uCurie DPM or kBq e Current Date e Half life of the Isotope For 1251 131T 32p 33P 35S and 3H the isotope is selected and the system automatically supplies the respective half life time For other isotopes please enter the corresponding half life time for the isotope Equation ACteorr actour acteur X 1 Exp 0 693 x actgays Ntime where aCteorr Corrected Activity act Current Activity aCtgays Difference in days hime Half life in days Half lives of Stored Isotopes 125 60 30 Days 131 8 10 Days P 14 28 Days 33P 25 40 Days 35S 187 40 Days 3H 4490 Days or 12 3 Years DU Series 700 User s Guide PN A24014 AA DNA Protein Tools Mode Calculations l 2 Calculations To enter this function Radioactivity Decay Correction ae 1 Touch Radioactivity Decay in the Calculations menu Current Activity mCi 21576 10 2 Touch Calculate to perform the calculation and display the result s based on the parameters set in Options Calculate Options Options 3 Touch Options to set the parameters for the calculation Original Date Original Activity mCi 21 MAY 2004 325000 0 4 Touch the parameter that identifies the value you want to 1 MEM 12 JAN 2005 60 3 D Ei using a numeric keypad to enter a value or Isotope Units ass unc e selecting the radio button that displays the desired value To select a date Optic Original Date ix 1 Touc
96. inate BCA 70 The following substances react with the Folin reagent tryptophan tyrosine most phenols uric acid guanine and xanthine This method is the same as the Lowry discussed above except that the samples containing more than 25 g ml protein are analyzed at 500 nm The Biuret method forms a blue copper complex under alkaline conditions From 10 to 1 200 g ml can be measured at 540 nm The Biuret method is less sensitive to amino acid composition than the Lowry method There are practically no biological substances with significant interference at pH 7 1 Virtually all proteins have an absorption maxima at neutral pH around 280 nm due to absorption by tyrosine Amin 275 nm phenylalanine lambda max 257 nm and tryptophan mnax 279 nm Since proteins differ in their content of these amino acids this analysis is only approximate unless the standards used to construct the standard curve are made using the same protein measured in the samples This assay is linear in the range of 50 to 3 000 g ml Proteins form a stable complex with colloidal gold which allows very small quantities of protein to be analyzed at 595 nm This assay 1s linear in the range of 5 to 200 ng ml The BCA assay involves the formation of the Biuret protein copper complex in alkaline solution This complex is then reacted with bicinchoninic acid BCA to form a water soluble salt that has a strong absorbance at 562 nm This assay is easier to
97. ing Lamps on page 142 Replace the visible lamp see Changing Lamps on page 142 Not enough air is allowed to flow near the source compartment Remove papers or other debris that are near the air vents on the back and underside of the instrument Press the START soft key Close sampling module lid and press the START soft key Insert sampling module and secure with module lock Close sampling module lid and press the START soft key Replace the deuterium lamp see Changing Lamps on page 142 Clear the message by pressing the CLEAR WARNING soft key It is possible to continue taking readings with the visible lamp only Replace the visible lamp see Changing Lamps on page 142 Clear message by pressing the CLEAR WARNING soft key DU Series 700 User s Guide PN A24014 AA Troubleshooting Other Error Conditions l 6 16 3 Other Error Conditions Table 16 2 Other Error Conditions Error Message Recommended Action The instrument will not Verify that the power cord is securely power up plugged into the power outlet and the back of the instrument Check fuses see Changing the Fuse on page 144 The screen is not readable Turn the contrast knob to the right of the screen until the screen is clear The wavelength is not The instrument was powered up with a accurate sample solution in the sampling module Remove the sample and power up the instrument again Graphics are not pri
98. ing the reading sequence the Carousel turns back to the initial position The screen reactivates the Blank Read buttons NOTE You may call the Carousel Options screen at any time to set the Carousel options in an instant by touching the Carousel Icon see arrow Alternatively you can go through the Options button for this function NOTE Entering the mode or changing scanning parameters requires a new baseline scan or blank scan After performing the baseline scan the instrument is ready to scan samples After starting the Reading sequence the screen replaces the Blank Read buttons with a Cancel button NOTE Touch Cancel at any time to start over and erase all scans from the current set of measurements You may touch the Carousel Icon see arrow to change the Carousel Settings in an instant without returning to the Instrument Setup menu After finishing the reading sequence the Carousel turns back to the initial position The screen reactivates the Blank Read buttons DU Series 700 User s Guide PN A24014 AA Ways Ci m am z am Select Yiew Cell Number C 4 2 3 v Kinetics Time Kinetics Time T DU Series 700 User s Guide PN A24014 AA T jare JN 0 Carousel Sipper and Peltier Operation Carousel Holder l 3 To display a graph scan or table tabular data from the available scans touch Options and then Select View Select the Cell Number by touching a radio button a
99. ith a blank solution into the cell holder and close the cell compartment recommended To blank against air use an empty cuvette or leave the cell holder empty NOTE f the lid of the cell compartment is open the instrument disables the Blank Read buttons 2 Touch Blank to blank the instrument The screen displays the Blanking message in the bottom left corner of the screen OF MAR 2005 21 17 29 SCA x 3 When the system has been blanked insert the first standard Read Standards cuvette into the cell holder and close the cell compartment m g mL Met l 0 1500 0 263 4 Touch Read to start the reading The screen displays the 0 2500 0 450 Reading message to the right of the concentration and O 5000 0 953 adds the reading Net Abs to the line with the respective concentration value 1 0000 NOTE Make sure you insert the standard cuvettes in the right sequence 07 MAR 2005 21 18 22 based on the entered concentration NOTE During the reading process the Read Blank buttons are replaced by a Cancel button You may touch Cancel to stop and discard the current reading 5 Continue until all standard cuvettes have been read and an absorbance value is associated with each concentration DU Series 700 User s Guide 65 PN A24014 AA Single Component Analysis Mode SCA Reading Standards After reading the last standard the system calculates and displays the standard curve 600 0 nm e Edit Stds go
100. leave the cell holder empty NOTE If the lid of the cell compartment is open the instrument disables the Blank Read buttons 3 Touch Blank to blank the instrument The screen displays the Blanking message in the bottom left corner of the screen DU Series 700 User s Guide PN A24014 AA Kinetic Time Mode Analysis of a Kinetic Run 1 Kinetics Time Peter 4 When the system has been blanked insert the sample cuvette into the cell holder and close the cell compartment 5 Touch Read to start the kinetics run The screen displays the Reading message in the bottom left corner of the screen with the count down for the remaining time before the next data point is taken NOTE During the reading process the Read Blank buttons are replaced Next Reading 00 07 by a Mark and a Stop button You may touch Stop to stop and discard the run in progress Options e Mark lets you mark the next data point collected The instrument does not use this mark it is provided so you can indicate a significant event such as the addition of a sample or other reagent The mark is also shown in the table e Stop ends the kinetic run and discards the data 7 3 Analysis of a Kinetic Run When the kinetic run completes the instrument does the following e Activates the sound emitting an acoustic signal to let you know that the run is complete e Displays the graph over the entire time total time e Scales the y axis depending on the
101. lengths and toggle background correction on and off When background correction is on you can modify the default background wavelength Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings 83 Nucleic Acid Analysis Parameter Setup Touch More to go to the Options screen Options e Concentration Off On allows you to switch the panum uias concentration calculation on or off You can also set the Path Le nath tem Factor and select the Unit in this screen e Concentration Format sets the number of significant digits Save as for the calculated concentration e Path Length cm allows you to modify the default path length of 1 cm if you want to use small path length cells for very high sample concentrations Instrument 5etup Return e Store Data Off On lets you toggle the storage setting and manually store data e Save as User Program stores the selected parameters as a user program see User Programs on page 43 84 DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Parameter Setup dsDNA ssDNA and RNA Touch Options for the parameter setup Nucleic Acid Analysis ds DNA More displays further options in the Options screen e 1 e 3 0 View Conc Abs lets you toggle between the screen that m g mL Y displays the result data concentration and the screen that Metano CODE
102. merical subscripts and superscripts after touching this key e 123 numeric Use this key to switch to a numeric keypad when you need to enter regular numbers The central part of the keypad changes to reflect the chosen entry mode To enter a character you must repeatedly touch a key until the desired character appears on the screen To enter a space use the underscore on the YZ_ key The keys to the right side of the screen are e CE clear entry Clears all text displayed in the entry field e Left Arrow backspace Moves the cursor back one position deleting the previous character e Right Arrow advance Advances the character to display the next one when the key shows more than one character DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 Instrument Setup Mode To change to Instrument Setup Mode select Instrument Setup in the Main Menu Instrument Setup Operator ID i Sample ID lt Off gt lt Off gt gt i The Instrument Setup menu displays a list of options you can use Date amp Display amp d Qu EPI to set instrument functions If the instrument recognizes a Sipper module or a Peltier module Y Lamp fe Control USB Port the Carousel Options key is replaced by Sipper Options or Operator ID Instr eet Operator iB Use the Operator ID screen to enter up to 30 sets of operator initials up to five characters each into the instrument You can
103. minutes minimum 5 Flush with deionized water for 1 minute 6 Flush with 10 Trace Klean solution for 2 minutes minimum See NOTE below 7 Flush with deionized water for 1 minute 8 Leave the Flowcell filled with deionized water DU Series 700 User s Guide PN A24014 AA Maintenance Cleaning Requirements l 5 NOTE To remove protein deposit from the inside of the Flowcell rinse the Flowcell with a 10 Trace Klean solution at 56 C for 15 minutes Cleaning Procedure Severely Contaminated Flowcells Occasionally a Flowcell may become severely contaminated with substances which have dried on the interior surfaces Standard cleaning procedures may not clean these Flowcells To clean them flush with 50 hydrochloric acid 6 normal for ten seconds then follow immediately with a 1 minute flush using deionized water Follow this with the cleaning procedure described in Cleaning Procedure Contaminated Flowcells on page 140 WARNING When handling hydrochloric acid always use protective A clothing and chemical safe goggles to prevent skin and eye contact Ensure that the working area is well ventilated to avoid inhalation of vapors In case of contact immediately wash affected area with running water for 15 minutes For eyes also contact a physician immediately Other information It is important that the Flowcell never be left to air dry The Flowcell should be flushed and filled with deionized water when not in use The
104. mory To send scan data from the Recall Data screen Highlight the line with the desired scan Touch Options Touch Send Data USB Port icon The instrument immediately sends to the connected devices the data of the selected scan NOTE You may repeat this procedure for the remaining scan data you want to send to the target location s The instrument automatically sends the data as a single WLDATA file to the memory device using the CSV Comma Separated Value file format The file name uses the following format scanData X csv where X is the Scan 1 20 NOTE CSV files are the preferred format for data import into spreadsheet and graphing programs as well as statistical packages DU Series 700 User s Guide PN A24014 AA Sending Kinetic Data Kinetics Time Options Scale amp Units F LM Return Recall Data O9 MAR 05 2 04 27 O9 MAR 05 02 05 53 O9 MAR 05 2 07 31 Run 3 S60 nm O9 MAR 05 02 08 40 Run 4 560 nm 1 min Return Instrument Setup Kinetics Time al Options Store Recall Send and Delete Data Deleting Data Scans and Kinetic Runs l 4 You can send kinetic data to a printer or a memory device using the available USB ports Since the system automatically senses connected devices it sends the data to all available devices To send kinetic data directly from the Kinetics Time mode Touch Options Touch More Touch Send Data USB Port icon The instrument sends
105. n extinction coefficients fram amino acid sequence data Anal Biochem 182 319 326 1989 Most functions provide additional information such as references or calculation descriptions When extra information 1s available the Info button 1s enabled To access this information touch Info Protein Concentration from Amino Acid Sequence Data Determining specific absorptivity constants a and the concentration for synthetic or recombinant proteins or peptides is a necessary component of biopharmaceutical production and formulation Once an a value is determined for a particular protein in a well defined formulation matrix the concentration of that protein in solution can be rapidly determined from its measured absorbance and the specific absorptivity or extinction constant using a derivative of Beer s law This function of the DNA Protein Tools calculates the following parameters e Molar Extinction Coefficient or Absorptivity Constant e Protein Extinction Coefficient e Protein Concentration in mg ml The calculation is based on the following input parameters e of Thyrosines e of Tryptophans e of Cysteines or Cystines e Molecular Weight of the Protein e Absorbance at 280 nm e Dilution Factor NOTE The absorbance measurement must be taken separately 1Gill S C von Hippel P H Calculation of protein extinction coefficients from amino acid sequence data Anal Biochem 182 319 326 1989 104 DU S
106. n set the background wavelength by touching BKG NOTE With background correction active the analysis subtracts the absorbance reading at the background wavelength Abspy from the absorbance reading at the analytical wavelength Abs The system reports the net absorbance readings Abs et and uses them for all calculations AbSnet Abs Abspke Stan To change the unit touch Units in the Standard Curve Setup nits screen mg mL e To select an existing unit touch the line scroll down if necessary e To enter a new unit touch New and enter the unit using the alphanumeric keyboard e To delete a unit touch its description to highlight it then touch Delete NOTE The pre defined units are fixed You may delete only user defined units 62 DU Series 700 User s Guide PN A24014 AA Single Component Analysis Mode SCA Parameter Setup S If you had selected Standards Setup the SCA screen appears Use this screen to enter the known concentration for each standard SCA VIS 600 0 nm Enter Concentration mug mL Met By default the first line 1s highlighted After you confirm a 0 5000 concentration entered with the numeric keypad the screen highlights the next line automatically for the next entry NOTE You can highlight a desired line at any time by touching it if you need to edit or enter a concentration or modify a specific line Edit Delete Delete Edit Conc lets you edit or enter the concen
107. nal background wavelength The Double Ratio amp Concentration method allows you to specify three analytical wavelengths and an optional background wavelength The results include e Absorbance ratio of A A5 e Absorbance ratio of A4 A3 e Concentration A of 260 x factor These three methods allow you to calculate a 260 280 absorbance ratio with the optional use of background correction at 320 nm You can change each of these wavelengths The concentration is estimated in units of g mL by multiplying the absorbance of the analytical wavelength by a factor 79 Nucleic Acid Analysis Method Description The default factor is 50 0 for the dsDNA method 33 0 for the ssDNA method and 40 0 for the RNA method It is suggested that the default factor be used However you can change the factor Oligo DNA Long and Oligo RNA Long These two methods allow you to calculate the purity absorptivity extinction coefficient concentration and melting temperature DNA only based on the base composition and the absorbance at 260 nm For equations see Calculations on page 91 These methods use 260 and 280 nm as the analytical wavelengths and 320 nm as the optional wavelength for background correction You may change the second analytical wavelength A and the background wavelength The analytical wavelength of 260 nm is used to determine the concentration and cannot be changed NOTE Long oligonucleotides are considered those wit
108. ncentration factor 97 Nucleic Acid Analysis Calculations 98 DU Series 700 User s Guide PN A24014 AA 11 1 Method Description DU Series 700 User s Guide PN A24014 AA Jo Dye Incorporation Method Description l Jo Dye Incorporation The Dye Incorporation mode performs the Analysis of Labeling Reaction for Spotted Array Sample Preparation Reference Microarray Resource Facility Mount Sinai School of Medicine Protocol by Te Hua Tearina Chu Ph D The Dye Incorporation mode has been developed for single and duo color methods spotted array It is suitable for any dye that gives similar fluorescence wavelength to Cy3 550 nm or Cy5 650 nm Typical Procedure 1 Usea Beckman Coulter 50 ul Microcell to analyze the entire undiluted sample 2 Wash the microcell with water and dry it completely before use 3 Pipette sample into microcell and place microcell into the 50 ul Microcell Holder 4 Measure sample s using the Dye Incorporation mode 5 Pipette sample from the microcell back into the original tube Equations cDNA abs5go x volume x 37 ng uL x 1000 pg ng 324 5 pg pmol Cy3 absss x volume 0 15 Cy5 7 absgsox volume 0 25 Ratiocy3 cDNA Cy3 Ratiocys cDNA Cy5 where Ratio Nucleotides Dye Ratio cDNA Nucleotides cDNA in pmol Cy3 Cy3 Dye in pmol Cy5 Cy5 Dye in pmol abs g Absorbance at 260 nm absssy Absorbance at 550 nm absgsy Absorbance at 650 nm vol
109. nd 5 0 nm Automatic Automatic based on method selection Depending on selected resolution 100 4500 nm min 3 nm 0 3 to 3 0 A or 0 1 to 100 T 0 005 A at 0 0 to 0 5 A 1 at 0 5 to 2 0 A lt 0 5 at 2 0 A 1 at gt 2 0 A KI Solution at 220 nm gt 3 3 Abs DU 700 is lt or 0 05 T max at 220 and 320 nm 18 2 Physical and Environmental Specifications Width Height Depth Weight Operating Requirements Storage Requirements DU Series 700 User s Guide PN A24014 AA 17 7 in 450 mm 7 9 in 200 mm 19 7 in 500 mm 34 2 Ibs 15 5 kg 10 40 C 50 104 F max 90 relative humidity non condensing 25 60 C 13 140 F max 80 relative humidity non condensing 159 Specifications Power and Other Specifications 18 3 Power and Other Specifications Power Ports Cable Water resistant to 160 100 120 V 200 240 V 50 60 Hz automatic changeover USB 1 1 USB cable lt or 3 meters WARNING To ensure compliance with EN 61326 and USB 1 1 requirements the USB cable must not exceed 3 meters IP 32 DU Series 700 User s Guide PN A24014 AA Replacement Parts Service Centers and Warranty Replacement Parts Supplies and Accessories l O Replacement Parts Service Centers and Warranty 19 1 Replacement Parts Supplies and Accessories DU Series 700 User s Guide PN A24014 AA Table 19 1 DU Series 700 Instruments A23615 A23616 DU 720 General Purp
110. nd then touch Table or Graph to display the scan data in tabular form or its graphical representation After blanking the system the instrument is ready to start the kinetics run After starting the Reading sequence the screen replaces the Blank Read buttons with a Mark and a Stop button The Mark button enables you to place a marker a small black square at the current point as the instrument displays a line while reading the sample NOTE Touch Stop at any time to start over and erase all readings from the current set of measurements You may touch the Carousel Icon see arrow to change the Carousel Settings in an instant without returning to the Instrument Setup menu After finishing the reading sequence run the Carousel turns back to the initial position The screen reactivates the Blank Read buttons This completes the kinetic run Readings in all defined carousel positions are taken at each time interval For example the 6 defined carousel positions provide 6 kinetic runs Touch Options and Select View to select the kinetic run you want to display and analyze 119 Carousel Sipper and Peltier Operation Sipper Module 13 2 Sipper Module For information on changing sample modules loading and inserting the Sipper Module or setting the sipper parameters see Sipper Module on page 19 In general the operation is similar to measurements with a one cuvette cell holder The only difference is that
111. nd ug mL using the equations Conc pM pL Net Abs x Dil Factor ojigo X Pathlength 11 Conc pg mL Net Abs x Dil Factor Kojgo X Pathlength 12 where Net Abs Net absorbance at 260 nm calculated using equation 1 Dil Factor Dilution factor input by the user E oligo Molar extinction coefficient calculated using equation 6 7 8 or 9 K oligo Extinction coefficient calculated using equation 10 NOTE These concentrations are calculated using molar extinction coefficients which were obtained from absorbance measurements at 260 nm as described in the literature Therefore the wavelength used for concentration calculation is fixed at 260 nm and cannot be changed for that reason DU Series 700 User s Guide 95 PN A24014 AA Nucleic Acid Analysis Calculations Melting Temperature Oligo DNA Long Oligonucleotides longer than 30 bases are considered long oligos Tm 81 5 C 16 6 x log4o salt 1000 675 Lo1igo 0 41 x GC 13 where salt Millimolar salt concentration lt 1M user input Loligo Number of bases in the oligonucleotide GC GC content in the oligonucleotide expressed as a percentage Melting Temperature Oligo DNA Short 96 Oligonucleotides shorter or equal 30 bases are considered short oligos Tm AZH x 1000 AZS R x In C 4 273 15 16 6 x log o salt 1000 14 where AH Nearest neighbor enthalpy A
112. ngth of time in use Typically you might turn the instrument on for the entire 8 10 hour shift and then off until the next day NOTE In general avoid on off cycles of the lamp this shortens the lamp s life span For maximum life turn the lamp off only if it will remain off for at least 4 5 hours If the instrument needs a lamp for the selected program or the instrument is operating inside the lamp s spectrum the lamp switches on automatically DU Series 700 User s Guide PN A24014 AA Installation Instrument Setup Mode 3 ee Use the Lamp Control screen to set the lamp timer switches Lamp Control vVIS Lamp Lv Lamp 1 On C On Off Off 2 Select On to switch on the VIS Lamp a Save Save 3 To select the time for automatic lamp shutoff 2 Hours Hours a Select the Save check box located below the VIS Lamp Lernen posse us or UV Lamp control option Depending on your selection the screen displays either the Visible Lamp Cancel OK Save screen or UV Lamp Save screen b Selectthe length of time you want the lamp switched on Yisible Lamp Save c Touch OK Touch Lamp Control in the Instrument Setup menu NOTE After this period of time the lamp automatically turns off under one of these conditions 1 Hours 2 Hours e when no activity has taken place or 4 Hours e when the measurements have been outside from the lamp s 8 Hours wavelength range 12 Hours o TT A
113. nic components from overheating which helps to extend the life span of the instrument WARNING The cover can become hot especially when a deuterium lamp is used Do not place anything on top of the cover For information on replacing halogen and deuterium lamp see Changing Lamps on page 142 1 Remove the DU Series 700 Spectrophotometer and accessories from the shipping container 2 Inspect each item for any damage that might have occurred during shipment 3 Verify that all items listed in Standard Accessories are included If any items are missing or damaged contact your regional Beckman Coulter office or distributor 4 Do not send the instrument back without previous arrangement 5 Place the instrument firmly on an even table surface The following conditions are necessary to ensure that the instrument runs smoothly and has a long life e Maintain an ambient temperature of 10 to 40 C 50 to 104 F for proper instrument operation e Maintain the relative humidity at less than 90 moisture should not condense on the instrument e Leave at least a 15 cm 6 inch clearance at the top and on all sides for air circulation to avoid overheating electrical parts NOTE Protect the instrument from temperature extremes including heaters direct sunlight and other heat sources DU Series 700 User s Guide PN A24014 AA System Description Power Up Applying Power 2 2 5 Power Up Applying Power e Plug the suppli
114. nted The communications parameters are not set properly properly or graphics are not compatible with the selected printer Instrument locks up Verify that the OUTPUT mode is turned off during printing if no device is available to accept data DU Series 700 User s Guide 149 PN A24014 AA Troubleshooting Other Error Conditions 150 DU Series 700 User s Guide PN A24014 AA System Check Call System Check from the Main Menu l vi system Check The DU Series 700 Spectrophotometer lets you verify instrument performance The instrument contains the programs for checking wavelength accuracy bandwidth photometric noise stray light photometric accuracy photometric repeatability and photometric stability 17 1 Call System Check from the Main Menu You must provide the samples necessary to perform the stray light and photometric accuracy and photometric repeatability tests Touch System Checks in the Main Menu to display the System E DENEN Checks screen Information Update The System Checks screen allows you to get system information aah and run a number of performance tests Lamp History Factory Service 17 2 Instrument Information ERMENERER Touch Instrument Information to display the model serial Instrument Information number and software version DU 730 S N 123456789012345 Instrument Yersion 0 08c ox DU Series 700 User s Guide 151 PN A24014 AA System Check Upgrading the Instrument Software
115. ntrol Modules The Sipper Sampling Module uses a peristaltic pump to aspirate samples into a flow cell for readings After the module takes a reading it returns the sample or dumps it to waste The Sipper Sampling Module provides improved measurement accuracy because the same optical characteristics exist for both blanking and reading and when comparing measurements of different samples The module eliminates errors that might occur from optical differences between individual vials because it takes every reading in the same vial 19 Installation Modules Figure 3 12 Sipper Module 2 Pump Tubing Clamp DU Series 700 User s Guide 20 PN A24014 AA Installation Modules 3 Sipper Module Installation Remove the Sipper Module from the shipping container and inspect for any damage that may have occurred during shipment All models are shipped with the following Sipper Module Sipper Accessories Kit see Figure 3 13 Figure 3 13 Sipper Accessories Kit 1mm Sipper Accessories Kit Ce Reon o ELT MN s OwaGeswrWennmpeddy 4 Simone Danwei E Ea Pump Tubing white 7 2 locking screws eS o DU Series 700 User s Guide 21 PN A24014 AA Installation Modules Figure 3 14 Sipper Module with Tubes in Place Pump Tubing white Outlet Connector from pump to drain Flow Cell Sample Inlet Tubing Drain Waste Tubing Before you install the Sipper Module in the DU Series 700
116. o not allow the solvent or sample solution to evaporate from the cell Evaporation usually leaves a deposit on the cell window which can require extensive cleaning 2 Ifthe cell cannot be cleaned immediately soak the cell in distilled water Do not soak the cell in a detergent solution as it can etch the cell windows 3 Clean the cell with a mild detergent The detergent must be a true solution and must not contain particulate matter Dilute 10 Trace Klean solution available from Beckman is recommended Rinse the cell immediately with distilled water Never let the detergent remain in the cell Never use a brush or other instrument which might scratch the sides of the cell CAUTION Non dilute Trace Klean is a highly alkaline solution and should be handled with care 4 To remove protein deposits soak the cell in dilute Trace Klean solution at 589C for 15 minutes Then rinse with distilled water 5 Forother hard to remove deposits wash with a solution made from equal parts by volume ethanol and 3N HCL Rinse immediately with distilled water Do not soak the cell in this solution for more than 30 seconds CAUTION Do not use highly alkaline solutions abrasive materials or hot concentrated acids to clean the cell 6 Dry the cell by inverting it and placing it in a cell rack For faster drying use a vacuum Do not blow the cell dry with air unless the air is known to be clean Most laboratory air sources have minute oil par
117. oles of Ends This function converts DNA sizes kb to DNA amounts The following parameters must be supplied e Amount of DNA in ug e Size of DNA in kb Equation EndSpmoi DNA g x pmol 660pg x 109pg ug x 1 N x 2 x kb 1000bp Endspmoi Result Ends in pmol DNA Linear DNA in ug DNA amp Number of nucleotides in kilobases kb The average molecular weight of a single nucleotide pair is 660 pg pmol The number of ends in a linear DNA molecule is 2 and the conversion factor from kilobases to base pairs 1s kb 1000 bp Molar Ratio of Insets to Vector for Ligations This function calculates the ng of insert for a 1 1 molar ratio The following parameters must be supplied e Length of Insert in kb e Length of Vector in kb e Amount of Vector in ng Equation insert insert vector x vectOramt where insert Result Insert in ng insert Insert Length in kilobases kb vectoryy Vector Length in kilobases kb vectOramt Vector Amount in kilobases kb Generally ligations are tested at 1 3 1 1 and 3 1 insert vector molar ratios DU Series 700 User s Guide 111 PN A24014 AA DNA Protein Tools Mode Conversions Nucleic Acid Concentration from Abs 260 This function estimates the DNA RNA Oligo concentration from an absorbance value NOTE You may also use the Nucleic Acid Analysis mode of the DU 730 to measure the sample and obtain the result estimated concentration at the
118. ong Nucleic Acid Analysis i Edit 260 0 280 0 Composition HS FEB ZUUS 18 17 03 Options Dilution X Salt Concentration 1 0000 50 000 Units Path Length cm pmol uL 1 0000 Store Data Save as Off 7 User Program Instrument Setup 86 Touch Options for parameter setup More displays further options in the Options screen View Conc Abs lets you toggle between the screen that displays the results data concentration and the screen that shows the raw data absorbance values NOTE View Conc Abs option becomes enabled after you enter the base composition Edit Composition lets you enter the base composition number of A C G and T U bases N stands for unknown bases lets you modify the A wavelengths and toggle background correction on and off When background correction is on you can modify the default background wavelength Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings Touch More to go to the Options screen Dilution X lets you enter a dilution correction factor The displayed results are corrected for dilution using the following equation Con Conc x Dilution Salt Concentration lets you modify the default salt concentration using the numeric keypad Units toggle between the calculation and display of the concentration units pgmol uL and ug mL Path Length cm allo
119. or the following options Sipper Options t Sip Time Settle Time e Sip Time The sip time in conjunction with the pump 2 sec 5 sec adjustment determines the amount of sample delivered to mem C VENDU the sample cell Enter the amount of time 1 99 seconds for E Auto the pump to run to aspirate the sample into the flow cell Settle Time The settling time defines how long the instrument waits between turning off the pump and taking a sample reading Use this interval to allow bubbles and Cancel Default OK sample turbulence to settle out of the light path Enter the amount of time 1 99 seconds the instrument waits after the sip time before taking a sample reading During this time the sample stops flowing and stabilizes Purge Time The purge time in conjunction with the pump adjustment determines the amount of air or rinsing solution pulled through the sample cell after a reading This cycle is optional you can program the Sipper to recover the sample or to send the sample to a waste vessel Enter the amount of time 1 99 seconds for the pump to run to empty the sample from the flow cell after the sample reading Purge Start Auto Manual If Purge is enabled use this option to toggle between Manual and Auto In Manual mode you must initiate the sample purge In Auto mode the module automatically purges the sample as soon as a reading is taken DU Series 700 User s Guide 41 PN A24014 AA Installation Instrument
120. orrection 0 0 RR 106 CONV ON oatsenmeta wean mederi Sate eae eL aU 108 Micrograms or dsDNA to Picomoles 0 0 0 eee 108 Example for Conversion Functions 0 0 cc cece eee eee 109 Picomoles of dsDNA to Micrograms and Nanograms ee aue 109 Micrograms mL of Oligonucleotides ssDNA to Picomoles uL 110 Picomoles uL of Oligonucleotides ssDNA to Micrograms mL 110 Micrograms of Linear DNA to Picomoles of Ends 0000 111 Molar Ratio of Insets to Vector for Ligations 0 0 0 eee eee 111 Nucleic Acid Concentration from AbsQ260 0 0 0 eee 112 Protein Molar Conversion 0 0 0 ccc cee eee eee eens 113 Protein Coding Capacity 0 eee IIR 114 Temperature Conversion 0 0 0 ccc ccc eee eee eee eens 115 MO NOS 115 Nucleotide Naming Conventions 0 0 ccc ce eee ees 115 Standard Genetic Gode xt o eet prc gees dete RPccbwewe E Re4evrirteerg 116 Amino Acid Codes and Masses issssese RR 116 DNA PFOIBIISIZOS tuetur o hrs rater dew or Ete Cr ba ST D rede dp egre Da atta 116 DNA Sequence Triplets Decoder 0 0 ccc eee ene 116 solubility Density and pl of Amino Acids 0 0 0 cc cece eee 116 Hydrophobicity of AMINO AGIOS im v tmc dew EE ntn Eucherius 116 Radiac iV DBIES c cese ost ence puro intere acannon xut nr aw ee
121. ose UV Vis Spectrophotometer DU 730 Life Science UV Vis Spectrophotometer Table 19 2 Sampling Modules A23619 A23621 Sipper Sampling Module Peltier Temperature Control Module Table 19 3 Cell Holders A24211 A23620 A23622 A23623 A23618 standard Cell Holder Carousel with 7 Cell Positions 90 uL Microcell Holder Turbidity Cell Holder Multicell Holder Table 19 4 Standard 1 cm Cuvettes 886506 79152 996492 980012 996493 980015 096494 Open Top Optical Glass 1 each Open Top Optical Glass 4 each Open Top Optical Glass 6 each Open Top UV Silica 1 each Open Top UV Silica 6 each otoppered UV Silica 1 each otoppered UV Silica 6 each Table 19 5 Standard 1 cm Semi Microcells Masked 033041 933040 933043 2 0 mm Pathwidth UV Silica 2 each 2 0 mm Pathwidth UV Silica 4 each 4 0 mm Pathwidth UV Silica 2 each 161 Replacement Parts Service Centers and Warranty Replacement Parts Supplies and Accessories 162 Table 19 5 Standard 1 cm Semi Microcells Masked 533042 4 0 mm Pathwidth UV Silica 4 each 517 056 4 0 mm Pathwidth UV Silica 6 each Table 19 6 50 uL Microcells 9232 0 50 uL Microcell 1 each 923450 50 uL Microcell 2 each 523451 50 uL Microcell 4 each 523452 50 uL Microcell 6 each Table 19 7 Long Pathlength 5 cm Cuvette 886510 Open Top Optical Glass 1 each Table 19 8 Data Output Accessories 977510 HP DeskJet Print w USB Port and PCL3 100 240VAC 51
122. ou can only view the standard curve you cannot edit it e Store Data stores the sample data see Store Recall Send and Delete Data on page 125 e Save as User Program stores the selected parameters as a user program see User Programs on page 43 DU Series 700 User s Guide 67 PN A24014 AA Single Component Analysis Mode SCA Analyzing Samples OF MAR 2005 21 25 28 68 600 0 nm mug mL 0 25 0 25 0 16 O22 23 391 OUT FN Optians This screen shows the results of one sample with three replicates The CV Limit option has been turned on and the sample is flagged because the value is outside the accepted limit NOTE For using a Carousel Cell Holder a Sipper or a Peltier Temperature Controller see Carousel Sipper and Peltier Operation on page 117 NOTE For printing and storing data see Store Recall Send and Delete Data on page 125 DU Series 700 User s Guide PN A24014 AA 9 1 Method Description Protein Assay Analysis Bradford Lowry high Cancel Select by Number Bradford Lowry High DU Series 700 User s Guide PN A24014 AA Protein Assay Analysis Method Description Protein Assay Analysis The Protein Assay Analysis mode provides pre programmed methods for common protein assays to calculate the amount of protein in a sample The standard curve can have up to 24 standards with known concentrations The data from the standards fit to either a linear or nonlinear q
123. p and materials for one year after delivery of the products to the original Buyer by Beckman Coulter and if any such product should prove to be defective within such one year period Beckman Coulter agrees at its option either 1 to correct by repair or at Beckman Coulter s election by replacement with equivalent product any such defective product provided that investigation and factory inspection discloses that such defect developed under normal and proper use or i1 to refund the purchase price The exceptions and conditions mentioned above are as follows a components or accessories manufactured by Beckman Coulter which by their nature are not intended to and will not function for ninety days are warranted only to give reasonable service for a reasonable time what constitutes reasonable time and reasonable service shall be determined solely by Beckman Coulter A complete list of such components and accessories is maintained at the factory b Beckman Coulter makes no warranty with respect to components or accessories not manufactured by it in the event of defect in any such component or accessory Beckman Coulter DU Series 700 User s Guide 163 PN A24014 AA Replacement Parts Service Centers and Warranty Warranty 164 will give reasonable assistance to Buyer in obtaining from the respective manufacturer whatever adjustment is authorized by the manufacturer s own warranty c any product claimed to be defective must
124. pening at the front so you can read the name of the selected cuvette type directly 17 Installation Cell Holders 4 Secure the holder with two locking screws Figure 3 9 Installing the Multicell Holder Carousel Holder Sample Changer The Carousel Holder allows you to load up to seven cuvettes of solution into the instrument for analysis at one time The cuvettes can be various combinations of blanks and samples Use the Setup Mode to activate the Carousel Options and set up the number of cell positions used and the orientation of blanks and samples Figure 3 10 Carousel Holder Carousel Holder Installation To insert the Carousel Holder 1 Open the cell compartment 2 Place the Carousel Holder on the rotatable attachment on the bottom of the cell compartment so that the marking faces upward 18 DU Series 700 User s Guide PN A24014 AA Figure 3 11 Installing the Carousel Holder 3 3 Modules Sipper Module DU Series 700 User s Guide PN A24014 AA Installation Modules 3 3 Take care to position the holder exactly The markings on the holder and the rotatable attachment must line up exactly 4 Turn the holder slightly to the left or right until the guide key locks into position This establishes contact with the instrument For instrument setup options and procedures see Carousel and Module Options on page 40 This section describes how to install the Sipper and Peltier Temperature Co
125. plies and Accessories lisse sess 161 Repair Service Beckman Coulter Sales and Service Offices 163 VUES Screed 5 ocean ey nape CORRER 163 vill 1 1 General Information Proper Use About this Manual Product Compliance DU Series 700 User s Guide PN A24014 AA Introduction General Information Introduction The spectrophotometer has been designed in accordance with the current state of the technology and the acknowledged safety regulations The manufacturer certifies that this instrument was thoroughly tested inspected and found to meet its published specifications when it was shipped from the factory Nevertheless under certain circumstances users may be at risk or the proper functioning of the instrument may be impaired WARNING If risk free operation is not possible the instrument should not be switched on or it should be properly switched off and secured against being switched on unintentionally This 1s the case when The instrument is visibly damaged e An electrical failure occurs The temperature is above 70 C e Transport damage occurs The spectrophotometer is solely intended for carrying out individual measurements or series of measurements for laboratory analysis Beckman Coulter Inc cannot accept liability for any harm caused to persons or property as a consequence of using the instrument for any purpose other than those defined in the manual This manual cont
126. r The lid of the Sipper Module can be opened towards the back of the instrument Secure the Sipper Module and the Standard Cell Holder or Microcell Holder with two locking screws see Figure 3 13 Pull the pump adjustment forward 1 and open the pump tubing clamp 2 12 Wrap the white pump tubing around the pump and clamp the ends on the right and left in the front two retainers 3 NOTE The push on connectors of the pump tubing must be positioned as shown in the illustration 24 DU Series 700 User s Guide PN A24014 AA Installation Modules 3 Insert the flow cell 3 Use the outlet connector 2 to join the white pump tubing 1 to the flow cell outlet 3 Connect the drain tube 5 to the right end of the white pump tubing Connect the inlet tube to the inlet of the flow cell 4 Peltier Temperature Control Module The Peltier Temperature Control Module allows you to heat or cool the sample in the range of 15 C to 50 C 59 F 122 F set an alert for temperature deviation select units of centigrade or Fahrenheit and disable temperature control after a specified time You can set these parameters using Setup Mode Temperature control starts when you enter the temperature it continues until either you or the idle parameter turns off the temperature Figure 3 15 Peltier Module Peltier Temperature Control Module Installation To assemble the Peltier Module 1 Open the cell
127. r Using the Touch Screen The entire screen is touch activated touch screen Spend a few minutes touching various items on the screen to see how they work e Take time to touch the individual fields lightly to get familiar with their functions e To make a selection touch the screen with your fingernail fingertip pencil eraser or a stylus NOTE Only the supplied stylus ensures efficient use of the touch screen WARNING Do not touch the screen with a sharp object such as the tip of a ball point pen WARNING Do not place anything on top of the cover doing so could scratch it e Touch keys words or icons to select them e Use scroll bars to move up and down long lists very quickly Touch and hold the scroll bar then move your fingertip up or down to move through the list Highlight an item from a list by touching it once After you select the item the screen displays the selected item in reversed text light text on a dark background DU Series 700 User s Guide T PN A24014 AA System Description Design Ports and Power Figure 2 3 Ports and Power The power connector and power switch are locate on the back wall of the instrument The DU Series 700 Spectrophotometer has three USB ports as a standard feature They are located on the back wall of the instrument These USB ports enable you to output data and graphics to a printer or memory device 901606 ai EN Downstream B USB connector Two upstre
128. res that this is the case You may observe the following The UV lamp automatically turns on after you have entered a wavelength in the UV spectrum In this case you have to wait for the UV lamp to warm up before you can take readings During the warm up phase of the UV lamp the screen displays a Warming up message and flashes the UV lamp symbol When the UV lamp is turned on automatically the instrument performs the reading as soon as the UV lamp is ready MITIS ITE eh E TUTRUCESEEECIUREDEE The following methods have a result screen similar to the one Double Ratio amp Concentration shown here 0 I2 uisi Metzaao Conc 1 570 50 000 e 09 FEB 2005 18 16 35 ih Options 260 280 Ratio Single Ratio Double Ratio dsDNA ssDNA RNA For some of the methods you can toggle the view to display the raw data DU Series 700 User s Guide PN A24014 AA 89 Nucleic Acid Analysis Analysis of Samples 50 0 nm ef DTC Nucleic Acid Analysis Olgo DONA Long 14 140 Len Oils G T MN 12 1 0000 3 4 3 2 t EXEC Pw 0 1277 37104 Tm 8 FEB 2005 17 56 41 bh Optians 2 o0 0 nm Nucleic Acid Analysis Gligo ONA Short LSL sa Len Dils 1 1 0000 ACTTICAGCAGTU ExtC mw 0 1169 3699 7 O9 FEB 2005 18 04 25 FN Optians 90 The following methods have a result screen similar to the one shown here Oligo DNA Long Oligo RNA Long This result screen shows the following
129. rs must understand and follow all laws regarding the proper decontamination and safe disposal of electrical equipment Please contact your dealer or local Beckman Coulter office for details on the take back program that will facilitate the proper collection treatment recovery recycling and safe disposal of Beckman Coulter products bearing this label 4 DU Series 700 User s Guide PN A24014 AA System Description Systems and Functions 2 system Description 2 1 Systems and Functions The DU Series 700 Spectrophotometer is a complete scanning UV Visible spectrophotometer with a bandwidth of 3 nm and a wavelength range of 190 to 1100 nm The instrument comes with a complete set of application programs and multi language support The DU Series 700 includes two models DU 720 General Purpose e DU 730 Life Science The DU 720 contain the following modes e Fixed Wavelength e Wavelength Scanning e Time based Kinetic e Single Component Analysis The DU 730 contains the following modes e Fixed Wavelength e Wavelength Scanning e Time based Kinetic e Single Component Analysis e Protein Assay Analysis e Nucleic Acid Analysis e Dye Incorporation e DNA Protein Tools The system comes with a Standard Single Cell Holder for a 1 cm rectangular cuvette A test tube holder is fixed in the sample compartment Other sampling devices such as a 7 Cell Carousel a Sipper Module and a Peltier Temperature Control Module are optional
130. solating plug adapter e Never use a two wire extension cord or a non grounding type multiple outlet receptacle strip e Any servicing of this equipment that requires removing covers or panels can expose parts that may cause electric shock or personal injury Refer such servicing to qualified service personnel e Certain electrical circuits within this equipment are protected by fuses against over current conditions For continued protection against a risk of fire replace fuses only with the same type and rating specified DU Series 700 User s Guide PN A24014 AA Introduction Safety Precautions Chemical and Biological Safety Normal operation of this instrument may involve using toxic flammable or biologically harmful chemicals Users must take these precautions e Observe all cautionary information printed on the original solution containers prior to using them e Handle infectious samples in accordance with good laboratory procedures and methods to prevent spread of disease e Dispose of all waste solutions in a proper manner e When using hydrochloric acid to clean the flow cell observe standard laboratory safety procedures Wear protective eye covering and immediately wash any splashes from skin or clothing with plenty of water e Since concentrated Trace Klean is a highly alkaline solution handle it with care Source Lamp Safety The source lamps operate at high temperatures e To avoid a possible electric s
131. t touch the glass envelope on the new lamp If it is touched clean with alcohol 9 Screw in both fastening screws again until they are finger tight 10 Insert the deuterium lamp in the socket so that the safety contact clicks into place 11 Use a screwdriver to screw the back cover onto the instrument again 12 Plug in power supply again The Instrument is now ready for use Switch the instrument on 13 Reset the Lamp History see Lamp History on page 157 1 Switch the instrument off 2 Unplug from the mains electricity supply 3 Pull out the plastic base over the socket for power cable 4 Remove the defective fuse see Figure 2 3 on page 8 5 Insert the new fuse T 2 A L 250 V 6 Replace the plastic base 7 Plug in to the main electricity supply 8 Switch the instrument back on DU Series 700 User s Guide PN A24014 AA Maintenance Changing the Filter Pad l 5 15 4 Changing the Filter Pad Figure 15 2 Base of DU Series 700 Spectrophotometer with Filter Grid Filter grid Phillips screw Filter pad NOTE Empty the cell compartment NOTE Unplug the instrument 1 Turn the instrument over carefully and place it on a soft surface 2 Use a screwdriver standard or cross head to open the filter grid 1 3 Lift the filter grid 1 DU Series 700 User s Guide 145 PN A24014 AA Maintenance Changing the Filter Pad 4 Remove the old filter pad 3 and replace it with a new one 5
132. ter taking multiple scans the instrument stores the scans scan 4 423 453 nm 5 0 nm sequentially starting with the highlighted scan If there are scans already stored in subsequent locations the storage location will be overridden After reaching the maximum storage location 20 the instrument stores the remaining scans starting with scan 0 In this case stored scans will be overridden Cancel The system briefly displays the message Data stored and returns to the previous screen You can touch Cancel to return to the previous screen without storing the scan s 126 DU Series 700 User s Guide PN A24014 AA Store Recall Send and Delete Data Recalling Data Scans and Kinetic Runs l 4 Storing Kinetic Data Kinetics Time After completing the kinetic run touch the Options button and then the Store icon folder with arrow Kinetics Time 29 0CT 04 15 56 36 Run 1 570 nm The Store Data screen displays Touch the line Run where you 15 NOV 04 14 00 40 want to store the actual run and then touch the Store button with a the folder icon to place the kinetic data in storage Run 3 azl nm 15 NOV D4 15 07 18 The system briefly displays the message Data stored and Pun Aa returns to the previous screen You can touch Cancel to return to the previous screen without storing the kinetic data 14 2 Recalling Data Scans and Kinetic Runs Recalling Data This section applies to Fixed
133. the actual kinetic data immediately to the connected devices To send kinetic data from the Recall Data screen Highlight the line with the desired Run Touch Options Touch Send Data USB Port icon The instrument immediately sends the kinetic data of the selected run to the connected devices The instrument automatically sends the data as a single TCDATA file to the memory device using the CSV Comma Separated Value file format The file name uses the following format TCData_X csv where X 1s the Scan 1 20 NOTE CSV files are the preferred format for data import into spreadsheet and graphing programs as well as statistical packages 14 4 Deleting Data Scans and Kinetic Runs Deleting Data DU Series 700 User s Guide PN A24014 AA This section applies to the Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes To delete stored data Touch Options 2 Touch Delete The Delete Data screen displays 133 Store Recall Send and Delete Data Deleting Data Scans and Kinetic Runs 3 Choose whether you want to delete a single point selected item the filtered data or all data by touching the respective radio button 4 Touch OK to delete the data NOTE The number in brackets shows the total number of data assigned to this selection 134 DU Series 700 User s Guide PN A24014 AA Store Recall Send and Delete Data Deleting Data Scans and Kineti
134. the line scroll down if necessary e To enter a new unit touch New and enter the unit using the alphanumeric keyboard e To delete a unit touch its description to highlight it then touch Delete NOTE The pre defined units are fixed You may delete only user defined units If you had selected Standards Setup a screen with the selected method appears Use this screen to enter the known concentration for each standard By default the first line 1s highlighted After you confirm a concentration entered with the numeric keypad the screen highlights the next line automatically for the next entry NOTE You can highlight a desired line at any time by touching it if you need to edit or enter a concentration or modify a specific line Edit Conc lets you edit or enter the concentration using the numeric keypad e Delete Line removes the selected line The button is enabled only when a line with a concentration is highlighted e Delete Abs this button remains disabled until standards have been read and absorbance values are available DU Series 700 User s Guide PN A24014 AA Protein Assay Analysis Parameter Setup O ES This numeric keypad appears when you touch Edit Conc Concentration mg mL Enter the desired concentration and touch Next to enter the next value The system adds the concentration to the list 1n the background and highlights the next line Continue until all concentrations have been entered e Ne
135. tic mode the purge begins immediately after the reading without operator intervention At this time if the sample is going to waste you can place a demineralized water purge at the sample inlet to rinse the sample cell between readings DU Series 700 User s Guide PN A24014 AA Wavelength Scan Wavelength Scan PG 340 Sipping 5 sec DU Series 700 User s Guide PN A24014 AA Ed Test Cancel Optians Carousel Sipper and Peltier Operation Sipper Module l 3 Leave the inlet tube in the purge solution until the Sipper pump stops The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date NOTE If you need to stop the purge cycle during the purge interval touch Cancel When the sample purge is complete the instrument is ready for the next sample Place the sample inlet tube into the blank solution and touch Blank or Read Leave the inlet tube in the blank solution or the sample vessel until the Sipper pump stops and the settling cycle begins After starting the sipping reading sequence the screen replaces the Blank Read buttons with a Cancel button NOTE If you need to stop the sip cycle touch Cancel The instrument Skips the sip and settle cycles The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date When the settling cycle is complete the screen displays the Blank button e Ifthe
136. tic profile or the tabular data and calculate the rate or slope of a given time range 7 1 Parameter Setup Kinetics Time VIS To enter the Kinetics Time mode 1 Touch Kinetics Time mode in the Main Menu 2 Touch Options to set the parameters Time amp Interval More displays further options in the Options screen Store icon stores the kinetic data 09 NOV 2004 08 20 47 Time amp Interval lets you define the total time for data collection and the time interval between the collected data ptions points e lets you determine the wavelength View Table View Graph displays the tabular data or the graph By default the graph or kinetic profile appears The button becomes enabled after the run is complete Options 3 Touch More to go to the Options screen Sale PC uot Cr Scale amp Units lets you select Abs or T and determine the scaling of the graph manual or automatic e Send Data sends data to a printer computer and storage device NOTE For instructions on storing and printing scan data see Store Recall Send and Delete Data on page 125 Instrument Setup DU Series 700 User s Guide D7 PN A24014 AA Kinetic Time Mode Taking the Kinetics Readings Ki ri pr Fri ure SN Time amp Interval Total Time uno Reading Interval 10 Seconds Cancel OK t a ee Optir 7 E Units Abs Scale amp Units Scale Auto C Manual
137. ticles originating from the compressor pump NOTE If the cell is to be used immediately rather than drying the cell completely rinse the cell with the next sample solution then fill the cell The outside surfaces of the cell may be dried and lightly buffed using lens tissue or a soft lint free cloth DU Series 700 User s Guide PN A24014 AA Maintenance Cleaning Requirements l 5 Cell Deterioration There are two main causes of cell deterioration both of which result in reduced transmission through the cell e Films which are deposited by solvent evaporation strong wetting agents or inadequate cleaning These decrease the transmission properties of the cell and may cause contamination of subsequent samples e Etching caused by the continued use of strong alkali or concentrated mineral acids either in the sample or in the cleaning solution Etching is also caused by weak alkaline solutions left in the cell for long periods of time Etched cells have reduced transmission properties because light is scattered from the etched surfaces To detect the extent of cell deterioration measure the transmittance versus air at 220 240 and 270 nm silica cells or 320nm optical glass cells A new Beckman cell filled with double distilled water will have a transmittance of at least 80 0 1 abs Caution should be observed when using different cells for the blank or reference and the sample especially if the cells have d
138. tion The test at 340 0 nm requires a 50 g L aqueous solution of Sodium Nitrite NaNO gt Both of these solutions need to be measured in quartz cuvettes which transmit UV light 1 Touch A to select the wavelength 2 Makea choice and confirm with OK 3 Touch Blank 4 After the system has blanked insert the sample cuvette and touch Start DU Series 700 User s Guide PN A24014 AA Q tic Cai ee a i Stray Light Check Wavelength 340 0 nm 0 000 Abs Average 0 002 Abs Std Deviation 0 0017 Abs cancel Start AC Absorbance Check 0 tic rad uu uem P Absorbance Check Wavelength 546 1 nm 0 0000 Abs 1 of 10 cancel Read A oO tic zl o x Absorbance Check Wavelength 546 1 nm 0 000 Abs Average 0 0001 Abs Std Deviation 0 0001 Abs cancel Blank A DU Series 700 User s Guide PN A24014 AA System Check Optical Checks l vi When the test is complete the screen displays the results The instrument averages thirty readings for the blank and calculates the Average and the Standard Deviation from 100 consecutive absorbance readings The average of the readings is the stray light value in absorbance The stray light is typically about 3 3A which is the same as 0 05 T 5 Touch Cancel to return to the Optical Checks screen The Absorbance Check lets you test the photometric accuracy and repeatability of the instrument This test requires standard filters such as NIST S
139. tion to mark one fixed limit and use the second cursor to determine the other limit These limits determine the time range used to calculate the rate or slope displayed at the bottom left corner of the screen together with the corresponding r value correlation coefficient NOTE For instructions on using a Carousel Cell Holder a Sipper or a Peltier Temperature Controller see Carousel Sipper and Peltier Operation on page 117 NOTE For instructions on printing and storing data see Store Recall send and Delete Data on page 125 DU Series 700 User s Guide PN A24014 AA Single Component Analysis Mode SCA Parameter Setup S Single Component Analysis Mode SCA The Single Component Analysis SCA lets you calculate the concentrations from unknown samples containing a single component using a standard curve The standard curve can have up to 24 standards with known concentrations The data from the standards fit to either a linear or nonlinear quadratic curve This mode requires a standard curve before analyzing the samples You can specify the standard curve either by measuring standards with known concentrations or by entering the coefficients from a previous standard curve 0 1 Parameter Setup Ahi 10 enter the Single Component Analysis mode touch Single Component Analysis in the Main Menu Touch Standard Curve if you want to create a standard curve by measuring standards with known concentrations For deta
140. tions screen of Sample C Limit i Replicates 1 off e of Sample Replicates lets you enter the number of Standard Curve i a NOTE When analyzing two replicates the instrument calculates the c Save as average When analyzing three replicates the instrument calculates the eo eae mean and the coefficient of variation CV if enabled e CV Limit Off On If you select three replicates the CV Limits button becomes enabled Use this button to toggle Coefficient of Variation CV limit reporting on or off and to set a CV limit The sample result will flag samples outside of the specified CV limit with OUT e Standard Curve allows you to the Standard Curve setup parameters Instrument 5etup Return NOTE You can only view the standard curve you cannot edit it e Store Data stores the sample data see Store Recall Send and Delete Data on page 125 e Save as User Program stores the selected parameters as a user program see User Programs on page 43 Bradford Ur ELE This screen shows the results of one sample with three replicates Read Samples For this example the CV Limit option has been turned on because Sep Moa the value is outside the CV limit its value is flagged OUT 0 25 0 16 NOTE For using a Carousel Cell Holder a Sipper or a Peltier Temperature 0 22 Controller see Carousel Sipper and Peltier Operation on page 117 23 136 OUT ee NOTE For printing and storing data see Store Recall S
141. tration using the Cancel i Done Conc Line Abs numeric keypad e Delete Line removes the selected line The button is enabled only when a line with a concentration is highlighted e Delete Abs this button remains disabled until standards have been read and absorbance values are available Lito This numeric keypad appears when you touch Edit Conc Concentration mmg mL Enter the desired concentration and touch Next to enter the next value The system adds the concentration to the list 1n the background and highlights the next line Continue until all concentrations have been entered e Next steps forward in the entry list and displays the corresponding concentration if available e Prev steps back in the entry list and displays the mi ss BE E corresponding concentration if available e Cancel discards the current entry and returns to the previous screen When you are done entering all concentrations or making modifications touch OK to return to the Enter Concentration list Then touch Done to start reading the standard cuvettes and creating the standard curve DU Series 700 User s Guide 63 PN A24014 AA Single Component Analysis Mode SCA Parameter Setup Coefficients Setup Coefficients Setup Touch Coefficients in the SCA screen to display the Coefficients Define Setup screen You may choose the following options Coefficients ENTE Concentration Format Define Coefficients allows you to
142. ts Decoder also called the DNA Codons as they are read on the sense 5 to 3 strand of DNA Solubility Density and pl of Amino Acids Hydrophobicity of Amino Acids Radioactivity Units Metric Prefixes This function provides a table with the common amino acid names and list the solubility g 100g at 25 C the Crystal Density g ml and the isoelectric point pI at 25 C This function provides a table that indicates hydrophobicity of amino acids based on the following references Janin 1979 Wolfenden Kyte amp Doolittle and Rose This function provides a table with radioactivity units and the corresponding conversion information This function provides a table with metric prefixes DU Series 700 User s Guide PN A24014 AA 13 1 Carousel Holder Carousel Sipper and Peltier Operation Carousel Holder l 3 Carousel Sipper and Peltier Operation For information on changing sample modules loading and inserting the carousel see Carousel Holder Sample Changer on page 18 For details on activating the Carousel Holder and setting the carousel options see Carousel and Module Options on page 40 The table below lists the activated disabled conditions of Blank Read and Blank amp Read buttons under various Carousel settings Table 13 1 Shifting Activated Disabled Conditions for Carousel Settings Carousel Mode Initial State Display After Blanking Display B 1 Blank Read R 1 n Read Read
143. tubing should remain attached When use is resumed the Flowcell need only be emptied flushed several times the filled with sample At the end of the day follow the daily cleaning procedure described in Cleaning Procedure Daily on page 140 Short cuts in the cleaning procedure usually prove to be self defeating and should be avoided since a build up of contaminants may occur DU Series 700 User s Guide 141 PN A24014 AA Maintenance Changing Lamps 15 2 Changing Lamps Figure 15 1 Lamp Compartment 142 Changing the Tungsten Lamp A Deuterium lamp lamp socket Plug contacts for fan Plug contact for Deuterium Lamp Contacts of tungsten lamp with cable 1 Switch the instrument off 2 Unplug the power cord WARNING The instrument must remain switched off until you have finished changing the lamp WARNING Wait until the lamp has cooled 3 Use a screwdriver to remove the cover from the back of the instrument the screws may be slotted or cross headed 4 Place the cover and the attached fan carefully beside the instrument take special care with the fan cable DU Series 700 User s Guide PN A24014 AA Maintenance Changing Lamps l 5 5 Push the spring 2 up and remove the tungsten lamp 1 Cat No A23778 from the lamp compartment 6 Unplug both plug contacts 6 from the tungsten lamp WARNING Hold the lamp only by the lamp socket Avoid touching the glass 7 Push these plug conta
144. uadratic curve This mode requires a standard curve before samples can be analyzed You can create the standard curve either by measuring standards with known concentrations or by entering the coefficients from a previous standard curve Protein Assay Analysis provides methods described in the following sections e Bradford on page 69 Lowry High on page 69 Lowry Low on page 70 e Biuret on page 70 e UV280 on page 70 e Colloidal Gold on page 70 e Bicinchoninate BCA on page 70 The Bradford method for measuring total protein concentration is based on a colorimetric reaction between Coomassie Brilliant Blue G 250 and the protein in the sample The complex is formed in about 2 minutes and is stable for 1 hour A wavelength of 595 nm is used From 1 to 140 mg ml of protein can be measured There are few interferences This analysis 1s about four times more sensitive than the Lowry analysis The Lowry method for measuring protein concentration is a colorimetric procedure Protein is first reacted with an alkaline copper reagent then with the Folin phenol reagent at room temperature The blue copper complex is read at 750 nm for samples containing less than 25 mg ml protein This analysis is 10 to 20 times more sensitive than measurement at 280 nm and 100 times more sensitive than the Biuret analysis 69 Protein Assay Analysis Method Description Lowry Low Biuret UV280 Colloidal Gold Bicinchon
145. ucleic Acid Analysis mode i 260 250 Ratio Single Ratio 1 Touch Nucleic Acid Analysis in the Main Menu 2 2 Touch the line with the method of choice to highlight it or A ee Oa ve EUN M M d Ld touch Select by Number and enter the desired number eU AC rie A eiie A etn ae ap lees ee era 3 Touch Start to enter the selected method ERAS NOTE The name of the selected method appears on the top left side of the Oligo RMA Short i display in the following screens c Cancel Select by Number DU Series 700 User s Guide 81 PN A24014 AA Nucleic Acid Analysis Parameter Setup 260 280 Ratio and Single Ratio Touch Options for the parameter setup Nucleic Acid Analysis ds DNA e More displays further options in the Options screen e 1 e 3 0 e For 260 280 Ratio BKG Corr Off On lets you toggle n Hg mL aay background correction on and off The wavelengths are fixed HLITIOTI S Lane e For Single Ratio lets you modify the default wavelengths and toggle background correction on and off When background correction is on you can modify the default background wavelength EX Timer Icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings Metzsaa COncs 1 6837 50 000 093 FEB 2005 17 19 25 Touch More to go to the Options screen Options e Path Length cm allows you to modify the default path Factor 50
146. ume Volume in uL 99 Jo Dye Incorporation Parameter Setup 11 2 Parameter Setup Uo Dye Incorporation Cy3 Incorporation z50 0 A amp 50 0 esoo Pc O9 NOv 2004 09 40 40 Yolume pL 50 0 Path Length cm 1 0000 Save as 7 User Program Return 100 Nucleotides pi cDNA Cys B t EET ee Dilution X Conc 4 0000 Mass ww Optians Store Data Off Instrument Setup 1 Abs unit at 260 nm 37 ng uL for cDNA 324 6 pg pmol is the average molecular weight of dNTP NOTE gt 100 pmol of dye incorporation per sample and a ratio of 25 50 nucleotides dye molecule is optimal for hybridizations NOTE Low dye incorporation is often due to mishandled or aged Cy dyes You need to obtain fresh dyes and repeat the sample preparation To enter the Dye Incorporation mode 1 Touch Dye Incorporation in the Main Menu 2 Touch Options to set the parameters More displays further options in the Options screen Cy3 Cy5 toggles between the results of Cy3 and Cy5 Dilution X lets you enter a dilution factor The displayed concentrations are corrected for dilution using the following equation Conc Conc x Dilution lets you enter the wavelength s and allows you to turn the ratio on or off Timer Icon lets you set the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings 3 Touch More to see the
147. unctions as a backspace button NOTE For Oligo RNA Long the T Thymine button is replaced by the U Uracil button Touch OK when you are done After setting the analysis parameters you are ready to read samples NOTE Read is disabled until a blank reading has been taken NOTE This description assumes that Single Reading is selected default as the reading mode and that a cell holder that holds one cell is used the Standard Cell Holder that comes with the instrument For instruction on how to operate a Carousel Cell Holder the Sipper Module or the Peltier Temperature Control Module see Carousel Sipper and Peltier Operation on page 117 DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Analysis of Samples Before taking measurements you need to blank the instrument using air no cuvette in the light path or a cuvette with a blank solution which is recommended for best results To read the samples 1 4 Insert the blank cuvette into the cell holder and close the cell compartment Touch Blank to take the blank reading When done the Read button becomes enabled Insert a sample cuvette into the cell holder and close the cell compartment Touch Read to take the sample reading NOTE Ifthe lid of the cell compartment is open the instrument disables the Blank Read buttons When trying to read a Blank or a Sample the appropriate source must be turned on The system assu
148. ures but fresh solution should always be used for finial rinses Conditioning a new Flowcell A new Flowcell or a Flowcell that has not been used recently needs to be conditioned Conditioning will produce an even smooth flow of sample solution through the Flowcell and help prevent bubbles from forming To condition a Flowcell rinse with deionized water flush with air and then rinse with spectral grade methanol Flush with air again and then rinse with deionized water The Flowcell is now ready to use Cleaning Procedure Daily 1 Flush with 1 mL of deionized water 2 Flush with 2 mL of 10 Trace Klean solution WARNING Concentrated Trace Klean is a highly alkaline solution and should be handled with care Always wear protective goggles to protect eyes against splashing liquid In case of eye contact immediately flush with running water for 15 minutes 3 Flush with a minimum of 5 mL of deionized water 4 Leave the Flowcell filled with deionized water NOTE Before next use flush with methanol then with deionized water Cleaning Procedure Contaminated Flowcells This procedure should be followed if bubbles remain in the Flowcell if the Flowcell is known to be dirty if the results are not reproducible or if the results appear to be inaccurate 1 Flush with deionized water for 2 minutes minimum 2 Flush with methanol for 2 minutes minimum 3 Flush with deionized water for 1 minute 4 Flush with methanol for 2
149. velength OS 4PR 2005 18 23 54 DU Series 700 User s Guide PN A24014 AA 400 nm bh Optians Fixed Wavelength Mode Parameter Setup Fixed Wavelength Mode The Fixed Wavelength mode lets you collect data at up to 4 wavelengths You can take and display the data in absorbance or 5 transmittance and calculate the concentration of your samples using a factor or a formula e Absorbance measures the amount of light absorbed by the sample in units of Absorbance Transmittance measures the percent of the original light that passes through the sample and reaches the detector To enter the Fixed Wavelength mode touch Fixed Wavelength in the Main Menu Touch Options for Parameter Setup This screen provides the following options More displays more options in the Options screen Store Off On lets you toggle the storage setting from Off to On and manually store data 9o Trans Abs toggles between VoTrans Transmittance and Abs Absorbance display readings NOTE Abs is in place of Trans after you have switched to Transmittance Timer icon sets the timer Using the timer does not affect the readings that the instrument is taking The times are not stored with sample readings e lets you enter the wavelength settings NOTE The following sections describe how to set the wavelength s the formula and the coefficients or factors 45 Fixed Wavelength Mode Parameter Setup
150. with the sipper you don t have to change cuvettes The blank and sample solutions are sipped into the cell a flow cell and then returned or pumped to waste NOTE Make sure to route the drain tube to an appropriate drain or collection vessel when disposing the sample Fixed Wavelengths Measurements Fixed Wavelength Agzo 0 000 Sipping 7 sec 120 320 nm ai Optians This section applies to Fixed Wavelength SCA Protein Assay Analysis Nucleic Acid Analysis and Dye Incorporation modes Place the sample inlet tube into the blank solution and touch Blank or Read button Leave the inlet tube in the blank solution or the sample vessel until the Sipper pump stops and the settling cycle begins After starting the sipping reading sequence the screen replaces the Blank Read buttons with a Cancel button At any time you can erase all readings from the current set of measurements and start over by touching Cancel The screen displays the remaining time in seconds in the bottom right corner of the screen in place of the date NOTE If you need to stop the sip cycle touch Cancel During the sipping and reading process the screen replaces the Blank Read buttons with a Cancel button The instrument skips the sip and settle cycles When the settling cycle is complete the screen displays the Blank button e Ifthe purge is set up for a manual start the instrument waits for you to touch Purge e In the automa
151. ws you to modify the default path length of 1 cm if you want to use small path length cells for very high sample concentrations Store Data Off On lets you toggle the storage setting and manually store data Save as User Program stores the selected parameters as a user program see User Programs on page 43 DU Series 700 User s Guide PN A24014 AA Nuclr 4 ane EIN vanes SENE 27 50 9 nm Composition Options Oligo DNA Short and Oligo RNA Short Nucleic Acid Analysis Oligo DONA Short Edit 280 0 AzBO 0 Sequence 093 FEB 2005 18 17 15 DU Series 700 User s Guide PN A24014 AA Nucleic Acid Analysis Parameter Setup In the Composition Options screen touch the desired base button and enter the number of bases using the numeric keypad NOTE For Oligo RNA Long the T Thymine button is replaced by the U Uracil button Touch OK when you are done Touch Options for parameter setup More displays further options in the Options screen View Conc Abs lets you toggle between the screen that display the results data concentration and the screen that shows the raw data absorbance values NOTE View Conc Abs option becomes enabled after you enter the sequence Edit Sequence lets you enter the base sequence up to 40 bases N stands for unknown bases lets you modify the A wavelengths and toggle background correction on and off When background correction is on you can modify
152. xt steps forward in the entry list and displays the 1 2 3 corresponding concentration if available cancel are e e Prev steps back in the entry list and displays the corresponding concentration if available e Cancel discards the current entry and returns to the previous screen When you are done entering all concentrations or making modifications touch OK to return to the Enter Concentration list Then touch Done to start reading the standard cuvettes and creating the standard curve DU Series 700 User s Guide 13 PN A24014 AA Protein Assay Analysis Parameter Setup Coefficients Setup Coefficients Setup Touch Coefficients in the Protein Assay Analysis screen to Define A display the Coefficients Setup screen You may choose the Coefficients following options Units Concentration Format i ate mg mL 0 01 e Define Coefficients allows you to enter the coefficients ofa Save as 7 User Program known standard curve e A lets you enter the wavelength and turn background correction off default or on e Units allows you to select the desired concentration unit E and or define new units Return Setup e Concentration Format lets you determine the number of significant digits for the concentration values e Save as User Program stores the selected parameters as a user program see Store Recall Send and Delete Data on page 125 The Define Coefficients screen allows you
153. you must first scan the baseline performing a blank scan Changing any of the scanning parameters requires a new baseline scan After scanning the baseline the instrument is ready to take sample scans To enter the Wavelength Scan mode 1 Touch Wavelength Scan in the Main Menu 2 Insert the cuvette with a blank solution into the cell holder and close the cell compartment recommended To blank against air use an empty cuvette or leave the cell holder empty NOTE If the lid of the cell compartment is open the instrument disables the Blank Read buttons 3 Touch Blank to start the baseline scan The screen displays the Blanking message in the bottom left corner of the screen 4 When the system has been blanked insert a sample cuvette into the cell holder and close the cell compartment 5 Touch Read to start the scan The screen displays the Reading message in the bottom left corner of the screen NOTE During the scanning process the Read Blank buttons are replaced by a Cancel button You may touch Cancel to stop and discard the scan in progress When the scan is complete the instrument does the following 1 Displays the entire scan over the selected wavelength range 2 Scales the y axis depending on the selected scaling mode 3 Activates the cursor functions in the vertical navigation bar 59 Wavelength Scan Mode scanning Wavelength Scan Terea Nna Located on the right side of the scan

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