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BioDrop TOUCH / TOUCH PC/ µLite/ Duo

1. BACKGROUND CORRECTION e TO compensate for the effects of background absorbance caused by turbidity high absorbance buffer solutions and the use of reduced aperture cuvettes the BioDrop spectrophotometers can use background correction at a 320 nm e When used A320 is subtracted from A260 and A280 prior to use so that Protein concentration Factor 1 x Abs 280 Abs 320 Factor 2 x Abs 260 Abs 320 Ratio Abs 260 Abs 320 Abs 280 Abs 320 e The use of background correction can remove variability due to handling effects of low volume disposable cuvettes Version 2 0 59 PROTEIN UV MEASUREMENT PARAMETERS Set Pathlength and Dilution Factor to the required values Check above to see if background correction is required The default values for A260 Factor and A280 Factor are 0 76 and 1 55 respectively these can be edited by pressing the appropriate box Set Units to encompass the expected units Concentration of your samples a 4 b You may advance to the next screen at any time by pressing the forward arrow and return to the previous screen by pressing the back arrow Proben UY Parameleis integration Time Integration Time can be set as you wish The Sample Seed rns entered under Sample will the filename of any saved file Sample 0 j of j Set the outputs required in your method For more L men information see the section Saving and Printing TAKING A
2. uu hand column and automatically subtracted from all results X B B CyDye DNA To toggle between DNA amp dye parameters press the toggle icon on the options menu Cydye DNA measurements are Sample 1 DNA Concentration l wavelength scanning measurements to view the scan for a particular measurement press the scan button in the options 2 700 ua menu 300 4400 soo 600 100 X d S SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 49 TM CALCULATION The Tm Calculation application calculates the theoretical melting point from the base sequence of a primer It is done using nearest neighbour thermodynamic data for each base in the nucleotide chain in relation to its neighbour Breslauer et al Proc Natl Acad Sci USA 1986 83 3746 The data obtained are useful in both the characterisation of oligonucleotides and in calculating Tm for primers used in PCR experiments The ACGT U sequence entered in the method parameters is used to calculate the theoretical Tm the theoretical absorbance Absorbance units mmol and the conversion factor mg ml This is possible as the stability of a bent and twisted sequence of bases such as an oligonucleotide is dependent on the actual base sequence These calculated thermodynamic interactions between adjacent base pairs have been shown to correlate well with experimental observations The Tm Calculation application
3. USB Version 2 0 63 The sample data is saved to a USB memory stick in format that can be read by BioDrop spectrophotometers only Files in this format cannot be opened by Microsoft Excel or similar programmes Note Sample data will be saved to the BioDrop Samples directory on the USB memory stick if this directory is not present it will be created Warning when data is being written to the USB memory stick the LED will be lit DO NOT remove the memory stick at this stage otherwise data may become corrupted If you have completed your set of measurements exit the application which will close the file on the memory stick USB CSV The data is saved to a USB memory stick in comma separated variable CSV format allowing it to be opened directly using Microsoft Excel or other similar programmes Files in this format cannot be opened using the instrument Note To view the data displayed in the File Created Date and Time cells in a recognised format this will need formatting as described below File Created Right click in the appropriate cell and select Format Cells from the list select Custom dd mm yyyy h mm from the list on the right hand side see below and select ok Format Cells er Alignment Font Border Fill Protection Sample 15 04 2010 12 59 Type ddi mm yyyy himm dd mmm mmrm yy himm am pm h mm ss am pm h mm h mm ss ddirom h mm mm ss mm ss h mm ss Type the number Format code us
4. environmental toxicology water treatment and teaching There are numerous published methods and assays for these applications The icons described throughout this manual use the names quoted in the Table of Icons on page 80 if you are unsure of any of their functions please refer to this section For detailed descriptions of the functions of parameter boxes please refer to the Glossary of Boxes section Note Throughout this manual all screen shots are shown on a white background there is also a black background available USE WITH BIODROP RESOLUTION PC SOFTWARE When connected to a PC the BioDrop spectrophotometer can be controlled using the BioDrop Resolution PC software packages The BioDrop TOUCH PC variant has no touch screen user interface and must be controlled using Resolution software Operation using BioDrop Resolution PC software is described in the Resolution user manual or Resolution help file Version 2 0 12 FREQUENTLY USED ICONS ICON NAME FUNCTION E EMILE E 6 aan Returns to the previous screen in a sequence Confirms selection entry Saves and exits ICONS ON THE SAMPLE MEASUREMENT SCREEN Take reference Performs a reference measurement Take measurement Performs a sample measurement Opens the options menu on the sample Options arrow measurement screen ICONS ON THE OPTIONS MENU Takes the user from the sample measurement Method parameters screen to the first method parameter screen All
5. 2011 65 EU EU ROHS directive 2006 42 EC Machinery directive Standards to which conformity is declared include EN61010 1 2010 Safety requirements for electrical equipment for measurement control and laboratory use General requirements EN61010 2 101 2002 Safety requirements for electrical equipment for measurement control and laboratory use Particular requirements for in vitro diagnostic IVD medical equipment EN61326 1 2006 Electrical equipment for measurement control and laboratory use EMC Requirements EN ISO 12100 2010 Safety of machinery Basic concepts general principles for design This equipment has been tested and found to comply with the limits for a CLASS A digital device pursuant to part 15 of the FCC Rules Hazards and Warnings This section describes potential hazards which may exist in the operation of these units A number of warning labels and symbols are affixed to your instrument These symbols are used to inform you of potential dangers which may exist or where caution is required Before installing your new unit please take time to familiarise yourself with these warnings and symbols This instrument is subject to the following identified hazards This unit uses a Xenon lamp which is a high energy light source DO NOT look closely at the cuvette holder or the micro volume sample port when performing a measurement as prolonged exposure to the light source may result in permanent eye damage High volta
6. 500 0 nm Time can be set as required The Sample Seed entered under Integration Time Sample will be the filename used for any data file saved se automatically a You may advance to the next screen at any time by pressing ucoze 1 the forward arrow and return to the previous screen by pressing the back arrow Single Wavelength Data Parameters Set Factor Method as required enter Factor using numeric entry and Units using alphanumeric entry ma 100rml 2 3 Single Wavelength O AwePhm 0 ji of j Set the outputs required in your method For more ae information see the section Saving and Printing TAKING A MEASUREMENT To perform a measurement insert a cuvette containing the ae reference solution in the cuvette holder for uLite and Duo load reference directly on the ute sample port and press the reference button Remove and replace with a cuvette containing the sample For the ute sample port wipe 81 away the reference with a lint free cloth and load the mg 100ml 324 10 sample directly on the port When the sample is loaded press the Take Measurement button Note For assays where there is no established concentration factor calibration should be carried out using prepared standards see Standard Curve for details of how to perform this SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0
7. SERIAL KINETICS MEASUREMENTS Serial kinetics is the measurement of the absorbance of a single sample over a specified duration at a specified interval As the BioDrop TOUCH is capable of taking up to 1 reading per second serial kinetics measurements can be used for rapid rate reactions MEASUREMENT PARAMETERS af 4445 Lp nat f 200 0 nen Same 1 Ha of Samquies gt Wavelength can be set as you require The Sample Seed entered under Sample will be the filename of any automatically saved file No of Samples is described below Note When performing a serial kinetics measurement with more than sample the measurement proceeds as follows Sample 1 will be measured for the full duration at the specified interval after this is complete sample 2 will be measured for the full duration at the specified interval The measurement will continue in this manner until all samples have been recorded When measuring more than 1 sample all data will be overlaid at the end of the measurement and automatically saved to the instrument s internal memory Set the Delay time before first measurement Duration total measurement time up to 180 minutes Interval duration between readings from 1 second to duration and Integration Time that you require Note The integration time is determined by the interval i e the maximum integration time is half the interval time Version 2 0 27 Mode has options for Delta A Final A and S
8. and date set This can be changed by pressing Date and Time After the desired date and time have been entered select the tick to save and exit or the cross to exit without saving X Version 2 0 16 REGIONAL S The BioDrop spectrophotometer will arrive with the language set to English This can be changed by pressing the Language box the options are English French German and Spanish To save any alterations press the tick to exit without saving press the cross Data Output mes This is the default saving and printing settings that will be used in all application method parameters These can be overwritten in an application User Interface User Interface Allows the user to set the desired brightness level of the screen the alphanumeric text entry mode and the duration after which the screensaver will be displayed if required Theme sets the screen background to either Black or White Service The Service section is for use only by a trained service engineer or upon recommendation of a member of BioDrop technical support Version 2 0 17 INSTRUMENT SETTINGS The following options are included under instrument settings Instrument Information Instrument Information GioDrop amp poe NAR Instrument information displays the serial number user Serial Humber TON S interface UI version build and release dates and instrument LII Build U Ul Released Mar 25 2010 Control IC
9. e Extremes of temperature may require recalibration of the unit for optimal performance e Ifthe instrument has been stored in a cold environment then it should be allowed to come to room temperature before turning on the instrument to avoid compromising the internal calibration procedure e The instrument must be placed on a stable level bench or table capable of taking its weight with sufficient space around the instrument for air to circulate freely e The equipment is operated using an 18 VDC power supply adapter unit Always use the power supply adapter and mains cords supplied e Local mains power requirements are as follows o 100 to 240 VAC o 50or60Hz e The UK style mains cord plug has a user replaceable 3A fuse Replace only with the same rating and type 3A BS1362 e The unit maximum power rating is 5OVA e The instrument should be positioned so that the power supply cable may be readily removed in the event of a hazard or malfunction e Locate the instrument in an atmosphere free from dust and corrosive fumes Use the dust cover to further protect the instrument when not in use or powered Version 2 0 3 Instrument Connections USB connector for PC connection 18V power supply connector C WM S T USB connector for USB memory stick Version 2 0 Equipment Operation BioDrop TOUCH PC The BioDrop TOUCH spectrophotometer is available as a PC only variant which has no touch screen user interface and mus
10. load reference directly on the uLite sample port and press the reference button Remove and replace with a cuvette containing the sample For the ute sample port wipe away the reference with a lint free cloth and load the sample directly on the port When the sample is loaded press the Take Measurement button With Feature Detection set to Coarse Sensitive or Custom the sample measurement screen will display a table below the scan This table will display the Feature Type selected in the method parameters To manually add a peak or valley to the table position the cursor over the desired feature by either touching the feature or using the left and right cursors and press an empty cell in the table Note Details of how to perform overlays data manipulation and selecting saved files can be found in the Trace Manager section Version 2 0 26 KINETICS Kinetics measurements made using a UV visible spectrophotometer measure the change in absorbance at a single fixed wavelength over a specified period This can be used to provide useful information when an appropriate factor defined in a reagent kit protocol is applied Reagent test kits are routinely used for the enzymatic determination of compounds in food beverage and clinical laboratories UV visible spectrophotometric kinetic assays are considered one of the most convenient measurements for enzymatic assays since they allow the rate of the reaction to be measured continuously
11. version IC Version VOLOT16 Mar 25 2070 i XN x Instrument Settings Instrument Settings allows the user to J nstumentsentings 1 Collecta new temporary baseline This will be stored until E ID D rop amp the instrument is powered off 2 Save the temporary baseline This will become the C El Temporar Baseline 1 Januar 2010 daai ndal DID 3 Restore the original baseline If measurements show the Machine Life 258 Hours permanent baseline and be stored until overwritten temporary baseline to be poor quality the permanent Service Date 1 January 2070 P baseline can be restored t 4 View instrument life in hours 5 View service date set by an engineer Lamp Settings 3 lO Drop Lamp settings displays the current lamp status riot naald Daie 1A172010 To exit at any time press the exit button located in the renedim T ODDO 207 bottom right hand corner 108 E Teud Dp Ti 9 i a e Version 2 0 18 USER ACCESS Usemame Password Group The BioDrop spectrophotometer has an option to assign users different access rights These are set via the user access icon Note The User access icon is only available to users who ON SOImIniSt ate Rhe es Adding a user To add a new user to the instrument select Add user on the touch screen The BioDrop spectrophotometer can store up to 16 individual users Add User Access Parameters Each user is given a user name usin
12. 0 600 Enter the concentration of prepared standards using the numeric keypad Auto Print a Set the outputs required in your method For more information see the section Saving and Printing Printto Saveto Version 2 0 56 Standard Curve Calibration Insufficient data 3 M G BCA Calibration To create the standard curve when using replicates press the replicates button in the bottom right corner to take you to the screen shown below With Replicates off standards can be measured directly as described below 2 0 4 0 6 0 8 io y 0 75004 0 050 R 1 0000 8 B Note After all replicates have been taken for a standard pressing the replicates icon takes the user to the next standard that was specified in the method To create a standard curve insert the cuvette containing the reference solution in the cuvette holder and press the take reference icon Remove and replace with a cuvette containing the first standard replicate in the series and press the take measurement icon A single reference suffices for standard curve creation BCA Calibration 2 0 4 0 6 0 8 L1 y 0 75004 0 050 R 1 0000 8 8 Continue recording all standards replicates until the standard curve has been completed After the standard curve has been collected press the forward arrow to proceed to the sample measurement screen Standard Curve Standards To ignore any outlying sta
13. 24 WAVESCAN A measurement of absorbance or 96 transmission of a sample over a specified wavelength range is one of the most useful physical characteristics of a compound both as means of identification qualitative analysis and of estimation quantitative analysis The observed features arise due to the various electronic transitions that are possible within a molecule The BioDrop spectrophotometers offer a range of post scan data manipulation options including 1st order derivative enabling identification of multiple unresolved peaks 2nd order derivative enabling identification of peak shoulders inflections 4th order derivative which identifies both multiple peaks and inflections at the same time Smoothing utilises the Savitzky Golay algorithm to smooth data and increase the signal to noise ratio Enhanced which enhances features sharpening peaks and valleys MEASUREMENT PARAMETERS Use Max Wavelength and Min Wavelength to set the required wavelength range Set Mode and Integration time as required The Sample Seed entered under Sample will be the filename of any automatically saved file No of Samples f isdescribed below Note With Sample Overlays set to 22 all wavelength scans will be automatically saved to the instrument s internal memory and will be displayed in Trace Manager You may advance to the next screen at any time by pressing the forward arrow and return to the previous screen by pressing
14. a kinetic measurement commences Numeric entry This is used in nucleic acid and protein applications to compensate for the absorbance of highly concentrated samples Used in wavescan only this switches display of peak cursors on and off Peak cursors show vertical dashed lines displaying the measured peak height and horizontal dashed lines showing the peak width 86 Duration 1 30 Dye 1 Mame Extinction Coefficient 150 0 E 3 Feature Detection Feature Sort wavelength Feature Type Version 2 0 Numeric entry This is the duration over which a kinetic measurement is performed Used in Cydye DNA application only This is the first dye type used in the measurement Used in Cydye DNA application only This is the second dye type used in the measurement where applicable Numeric entry for Cydye DNA application only This is the extinction coefficient of the specified dye Note for dyes included in the BioDrop software these values are not editable and the box will be greyed out Numeric entry to 3 decimal places In concentration and nucleic acid measurements multiplying absorbance readings by this factor gives the concentration value In kinetic measurements the result is calculated by multiplying this factor by absorbance delta absorbance or the slope Used in wavescan measurements only This determines the sensitivity of the peak or valley detection i e sensitive will detect more peaks or valleys tha
15. menu This can be repeated to add up to 4 discrete sections Note Sections must be added in numerical order i e t1 must be added after tO t2 after t1 etc With sections defined the data displayed in the table below Sample Sample 1 Time 1 00 0 Abs 0 235 0 2 the scan is determined by the position of the cursor Only when the cursor is positioned in the section of interest will this data be displayed is uw 14 ves ew Aline of best fit can be added to any section by positioning the cursor in the desired section and selecting the add line of best fit button from the options menu Note Details of how to perform overlays data manipulation and selecting saved files can be found in the Trace Manager section SAVING AND PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 29 TRACE MANAGER OVERLAYING amp MANIPULATING WAVESCAN amp KINETICS FILES Trace Manager is the application used by the BioDrop spectrophotometers to overlay and manipulate wavescan and kinetics files Samples are loaded into Trace Manager as described below USING SAMPLE MANAGER Wavescan and kinetics files can be loaded directly into Trace Manager by selecting the required files from Sample Manager on the main screen This procedure is outlined below Sample Manager Page 1 of 1 a wien Date LLL EL tt ie E Highlight the required files by pressing on the appropriate row and loa
16. of manual saving and printing see the Saving and Printing section Version 2 0 47 CY DYE DNA The measurement of the labelling efficiency of fluorescently labelled DNA probes before 2 colour micro array hybridization ensures that there is sufficient amount of each probe to give satisfactory signals The data also provides an opportunity to balance the relative intensities of each fluorescent dye by adjusting the concentration of each probe before hybridization The DNA yield is measured at 260 nm whilst the incorporation of the dyes is measured at the absorption maxima This method is also useful for measuring the yields and brightness of fluorescently labelled in situ hybridization probes MEASUREMENT PARAMETERS Number of Dyes this can be set to 1 or 2 Dye 1 Name allows the user to select the dye used in the measurement the EE 1 150063 oO BioDrop spectrophotometers have 19 dyes pre programmed Correction Factor and the option for user entry using the Custom Dye option A Max Extinction Coefficient and Correction Factor are only editable when using the Custom Dye option You may advance to the next screen at any time by pressing the forward arrow and return to the previous screen by pressing the back arrow With Number of Dyes set to 2 the next method parameter screen allows the user to specify the second dye used in the measurement CyDye DNA If the measurement requires the calculation of DNA Concentration and
17. optical alignment Contact technical support Incorrect sample reference Check sample and reference for contamination Check sample and reference samples are not the same Incorrect cuvette material for measurement wavelengths Wrong pathlength selected in software For standard cuvettes ensure the beam goes through the sample fill cuvette with sample to 20mm from the base For micro volume sample platform check size and position of droplet For DNA applications check that the measurements at 230nm and 320nm are near O Possible stray light issue Contact technical support Insufficient sample in cuvette Cuvette in wrong orientation Cuvette material unsuitable for wavelengths used Concentration of sample too low or too high For best results the measured sample absorbance using a 10mm path length cuvette should ideally be between 0 1 and 2 0 A If absorbance is gt 2 A measurement is no longer in the linear range Particulates in sample Absorbance measurements will not be accurate in turbid samples Possible noise or measurement stability issue Contact technical support Check all sample paths are clear and clean dried on DNA Protein sample on the Micro volume head on the Duo and uLite units may cause start up calibration errors Check original 18V dc supply is connected and is fully engaged Report persistent failures to technical support Absorbance readings Check that the Absorbance displayed is being normali
18. symbols by pressing abc 123 and Au respectively It is possible to toggle between upper and lower case letters and through a list of symbols by pressing abc and Au twice Note The layout of the screen is dependent on the text entry mode set under User Interface in Settings The numeric entry box allows the user to include numbers in the method parameters Depending on the numeric box selected it may be possible to add both positive and negative numbers Where there are more than two options the user will be presented with a Sample 15 list If there are more than 8 options the user can scroll through these using Sample 16 Sample 17 either the page up and page down arrows or the scroll bar Sample 18 Sample 19 Note If a box only contains two options i e On or Off pressing the box on SORE en the screen will toggle between the options and not produce a combination Sample 21 box Version 2 0 15 SETTINGS Settings are accessed via the Settings button on the main screen see below x x L Applications Favourites Methods P U L Life Science Sample Manager Settings Logout Switch User Date and Time Regional Data Output amp 2 ep User Interface Instrument User Access Settings a Service Note If User Access has been selected the User Access Icon will only appear for users with Administrator privileges DATE amp TIME The BioDrop spectrophotometer will arrive with the UK time
19. the reference solution in the cuvette holder and press the reference icon Remove and replace with a cuvette containing the sample or load sample directly onto the uLite sample port and press the take measurement button A single reference suffices for subsequent analyses in the same series Note Pressing on the equation name allows the user to view the equation and the individual measurement results USING STANDARDS Equation E ditor Do vou want to exit without saving this 2 method SAVING AND PRINTING When performing a measurement using a method that includes standards the first press of the take measurement icon will produce a message box that prompts the user to insert a specific standard After all standards have been measured subsequent presses of the take measurement icon will perform sample measurements As methods developed using Equation Editor may have taken time to input the software will prompt the user to save the method before exiting Pressing the cross will return to the user to the results screen where they can save the method pressing the tick will exit without saving Details of method saving can be found below in the Saving Methods section For details of manual saving and printing see the Saving and Printing section Version 2 0 42 LIFE SCIENCE APPLICATIONS c i va Nucleic Acids Protein This contains two sub folders Nucleic Acids and Protein The contents of these sub fol
20. uses matrices of known published thermodynamic values and extinction coefficients to calculate Tm and the theoretical absorbance factor of an entered base sequence Tm is calculated using the equation Tm AH x 100 273 15 log salt AS 1 987 x log c 4 53 0822 where AH and AS are the enthalpy and entropy values respectively summed from respective 2 x 4 x 4 nearest neighbour matrices c is the Primer concentration of oligonucleotide pmoles ml in the calculated Tm or the measured concentration in measured Tm In the latter case concentration is obtained from the equation c Abs 260 nm x Calculated factor x pathlength multiplier x 10 000 MW Calculated factor and MW are defined below salt is the buffer molarity plus total molarity of salts in the hybridization solution moles l Weights for AS are indexed by adjacent paired bases A similar equation applies to weights for AH again indexed by adjacent bases Note Bivalent salts may need normalising using a multiplying factor of 100 because of their greater binding power THEORETICAL ABSORBANCE The Theoretical Absorbance is based on a calculation as follows For each adjacent pair of bases nearest neighbours an extinction coefficient weight is accumulated using a 4 x 4 table one for either DNA or RNA This total weight is doubled and then for each Version 2 0 50 internal base a counterweight is subtracted using another 1 x 4 table The end bases are exclud
21. 96 transmission or concentration measurements at a single specified wavelength Wavelength scan between two user defined wavelengths in the range 190 to 1100 nm The BioDrop TOUCH allows data overlay post scan data manipulation and user configurable peak and valley functions Measurements of Absorbance versus time to determine rate or end points The BioDrop spectrophotometers allow data overlay post scan data manipulation and user defined sectors Concentration measurement at a single wavelength determined by the generation of a calibration curve of known standards Allows users to create their own unique methods including calculations and thresholds 21 SINGLE WAVELENGTH The Single Wavelength application performs simple absorbance A and 96 transmission 96T measurements on samples measuring the amount of light that has passed through a sample relative to a reference this can be air MEASUREMENT PARAMETERS Set Mode to Absorbance 96T or Concentration Wavelength and Integration Time can be set as required eae y The Sample Seed entered under Sample will be the filename used for any data file saved automatically You may advance to the next screen at any time by selecting the forward arrow or return to the previous ample E screen by selecting the back arrow Set the outputs required in your method For more information see the section Saving and Printing DNA The Lite sample port has set pathle
22. C Displayed on the status bar This indicates that the xenon lamp has failed Displayed on the status bar This indicates that the instrument is performing a measurement Displayed on the status bar This indicates that the instrument is printing to the internal printer Displayed on the status bar This indicates that the instrument is printing via PVC When used in standard curve applications i e Lowry protein assay this toggles the sample measurement screen to display or hide the standard curve Used in standard curve applications to collect data from a group of replicates Commences a sample measurement A reference measurement must be taken prior to a sample measurement Commences a reference measurement 83 Used in text entry mode to move the cursor backwards Backspace delete Hacen left and delete any unwanted characters Used in text entry mode to move the cursor forwards Forward space right Selects lower case letters when in text entry mode Symbols Selects symbols when in text entry mode Selects upper case letters when in text entry mode Selects numeric entry when in text entry mode Used in the wavescan and kinetics applications This allows the user to overlay up to 8 samples data files and Trace Manager un to choose what type of data is displayed i e raw data smoothed data 1st derivative Used on the Sample Manager screen to access data stored on a USB memory stick Used in the opt
23. DENVILLE SCIENTIFIC INC a division of Harvard Bioscience Inc GioUrop E E A 1005369 1005366 1005363 BioDrop TOUCH TOUCH PC uLite Duo UV Visible Spectrophotometers User Manual www densci com lt info densci com Fax 908 757 7551 Order 800 453 0385 84 October Hill Road Holliston MA 01746 CONTENTS HEALTH amp SAFETY General Safety General Hazards Unpacking amp Installation Instrument Connections Equipment Operation Controls and Indicators Intended Users Instrument Preparation Post Run Procedures Performance Validation User Maintenance Troubleshooting Customer Support Contacts Service Repair or Return Disposal INTRODUCTION TO THE BIODROP SPECTROPHOTOMETER USE WITH RESOLUTION PC SOFTWARE FREQUENTLY USED ICONS PERFORMING A MEASUREMENT TYPES OF BOXES SETTINGS Date and Time Regional Data Output User Interface Instrument Settings Instrument Information Instrument Settings Version 2 0 o cO CO CO N aA Ul wn A A b gt PRP e e e e Pe xm om N ha ha hea hae ah KA CO CO CO N N N OA A wa o W N N O O O USER ACCESS Adding a user Editing a user Deleting a user Editing user access APPLICATIONS Single Wavelength Concentration via factor Wavescan Kinetics Trace Manager Overlaying amp manipulating wavescan and kinetics files Standard Curve Equation Editor LIFE SCIENCE APPLICATIONS Nucleic Acid Applications DNA RNA amp Oligo CyDye DNA Tm Calculation Protein Applic
24. MEASUREMENT To perform a measurement insert the cuvette containing the reference solution in the cuvette holder and press the take reference icon Remove and replace with a cuvette containing the sample and press the take measurement 60 icon A single reference suffices for subsequent analyses in the same series If Background is set to On the A320 result will be included in the left hand column and automatically subtracted from the displayed A260 A280 and A260 A280 results SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 61 PROTEIN A280 MEASUREMENT PARAMETERS lecce Select the Mode you require the BioDrop spectrophotometers have options for Christian Warburg BSA IgG Lysozyme Molar Extinction Mass Extinction and Pathlength E196 for Molar Extinction the user will also be required to 10 mm enter the molar extinction coefficient and molecular weight Dilution Factor and atomic units for Mass Extinction 1 000 Set Pathlength and Dilution Factor to the required values Check above to see if background correction is required Set Units to encompass the expected concentration of your samples Integration time can be set as you wish The Sample Seed entered under Sample will the filename of any Integration Time saved file Set the outputs required in your method For more information see the section Saving and Printing Internal P
25. METHODS The BioDrop spectrophotometers allow users to store methods to the both the instruments internal memory and to USB memory sticks The procedure for saving methods is described below After selecting the desired application and setting the required method parameters select the Save Method icon from the options menu on the sample measurement screen Set the desired file name and save location using the dialogue box shown below Pressing the Folder box produces a list of available save locations USB will only appear on the list if a USB memory stick is inserted Methods 1 Pressing the Method Name box allows the user to set the desired method name using alpha numeric text entry X Press the tick to save and exit or the cross to exit without saving METHODS SAVED TO THE INTERNAL MEMORY BioDrop Touch ie Pa Methods saved to the instrument s internal memory are Applications Favourites Methods stored in either the Methods or Favourites folders both of I 8 which are accessed via the main screen The BioDrop Life Science Sample Manager Settinas spectrophotometers are capable of storing up to 90 geo methods on the instrument s internal memory Logout Switch User Version 2 0 70 METHODS FOLDER amp FH amp amp Methods 1 Methods 2 Methods 3 J j Methods 4 Methods 5 Methods amp f f Methods 7 Methods S Methods 3 RENAMING METHOD FOLDERS N i Methods 1
26. Methods 2 Methods 3 Lo Lb L Methods 4 Methods 5 Methods 6 B Methods 7 En SW Methods 3 4 LOCKING SAVED METHODS l Methods 1 Methods 2 Methods 3 L L L Methods d Methods 5 Methods 6 L Methods 7 La L S Methods 3 Methods Methods 1 Single Wavelen LZ Kinetics w avescan Single ave Srandard Curve Version 2 0 The Methods folder is made up of 9 folders each capable of storing up to 9 methods The method folder icons have been designed to give the user an indication of the number of methods that are stored in that folder Using the Rename Folder icon on the options menu the left hand icon it is possible to rename any of the 9 method folders using alphanumeric text entry Using the lock folder icon on the options menu the centre icon it is possible to add pass code protection to any of the method folders Locked folders cannot be renamed and are indicated by a padlock Within a methods folder it is possible to add pass codes to individual methods and to lock them from deletion using the lock icon on the options menu the centre icon Locked methods can be unlocked by using the unlock icon on the options menu the right hand icon selecting the desired method and entering the correct pass code 71 DELETING SAVED METHODS Methods Methods 1 1 RN Within a methods folder it is possible to delete saved Single Sinica vao as methods using the delete icon on the
27. ON OF PROTEIN CONCENTRATION USING DIRECT UV METHODS The direct UV method of protein determination has a number of advantages over traditional colorimetric assays in that it does not rely on an external protein standard and the sample is not consumed in the assay However the presence of nucleic acid in the protein solution can have a significant effect due to strong nucleotide absorbance at 280 nm This can be compensated by measuring A260 and applying the equation of Warburg and Christian for the protein crystalline yeast enolase Equation 1 Protein concentration mg ml 1 55 x Abs280 0 76 x Abs260 1 Protein concentration Factor 1 x Abs280 Factor 2 x Abs260 2 The BioDrop spectrophotometers use default A260 and A280 factors of 0 76 and 1 55 respectively These factors can be edited so that the equation can be applied to other proteins Equation 2 Compensation for background dilution and pathlength can also be entered To customise Equation 2 for a particular protein the A260 and A280 values should be determined at known protein concentrations to generate simple simultaneous equations which when solved provides the two coefficients In cases where Factor 2 is found to be negative it should be set to zero since it means there is no contribution to the protein concentration due to absorbance at 260 nm The A260 A280 ratio also gives an indication of protein purity a ratio of 0 57 can be expected for pure protein samples
28. asurements BioDrop TOUCH and Duo respectively Therefore before performing sample measurements it is necessary to perform a reference measurement to correct for solvent and or cuvette effects This is done as follows 1 Insert a cuvette containing the solvent buffer in the cuvette holder 2 Press Take Reference 3 Whenthe reference is complete remove the cuvette containing solvent buffer from the cuvette holder and insert a cuvette containing the sample solution 4 Select Take Measurement 5 Repeat steps 3 amp 4 until all sample data has been collected See the section Saving and Printing for post measurement options Note A single reference will suffice for subsequent analyses for samples with the same solvent In regards to the uLite and Duo measurements are taken as followed 1 Load sample volume of a minimum of 0 5ul of reference in the sample port 2 Press Take Reference 3 Whenthe reference is complete remove the sample by wiping with a lint free cloth from the sample port and load sample of interest 4 Select Take Measurement 5 Repeat steps 3 amp 4 until all sample data has been collected See the section Saving and Printing for post measurement options Version 2 0 20 Single Wavelength Wavescan Kinetics Standard Curve Equation Editor Version 2 0 APPLICATIONS Applications CREE w avescan Kinetics Sinale wavelength x py Standard Curve Equation E ditor Absorbance
29. at hirii Paaametiers Set Wavelength and Integration Time as required The Sample Seed entered under Sample will be the file name of any file saved automatically Calibration can be set to Standards the user is required to prepare and measure standards or Manual the user inputs both the standard concentrations and standard absorbances Set Standards Replicates Curve Fit and Units as required in your application Set the concentration values for each of the standards using the numeric entry box Standard Curve Pee l ann memBme on 33 Set the outputs required in your method For more information see the section Saving and Printing Standard Curve Calibration To create the standard curve when using replicates press the replicates button in the bottom right corner to take you to the screen shown below With Replicates off standards can be measured directly as described below Note Pressing the save method icon before any standards have been measured will save the method parameters only Recalling a method containing method parameters only requires the user to construct a standard curve before measuring samples Sandad Cases To create a standard curve insert the cuvette containing the reference solution in the cuvette holder and press the take reference button Remove and replace with a cuvette containing the first standard replicate in the series and press the take measurement button A singl
30. at this wavelength When measuring RNA samples the A260 A230 ratio should be 2 0 Ratios lower than 2 0 generally indicate contamination with guanidinium thiocyanate a reagent commonly used in RNA purification and which absorbs over the 230 260 nm range A wavelength scan of the nucleic acid is particularly useful for RNA samples Version 2 0 45 BACKGROUND CORRECTION e TO compensate for the effects of background absorbance caused by turbidity high absorbance buffer solutions and the use of reduced aperture cuvettes the BioDrop spectrophotometers have the option of background correction at a 320 nm e When used A320 is subtracted from A260 and A280 prior to use so that Concentration A260 A320 x Factor Abs ratio A260 A320 A280 A320 Abs ratio A260 A320 A230 A320 e The use of background correction can remove variability due to handling effects of low volume disposable cuvettes Spectral scan of nucleic acid Concentration 2 bb g m a20 240 260 280 300 320 8 X B BH Note An absorbance maximum near 260 nm and absorbance minimum near 230 nm a flat peak near 260 nm and steep slope at 280 nm and very little absorbance at 320 nm MEASUREMENT PARAMETERS Set Pathlength to match the cuvette being used and Dilution Factor if required If using low volume cuvettes set Background correction to on Set Units to encompass the expected concentration of your samples the default Factor will update auto
31. ation removing a USB memory stick before exiting will result in loss of data Note All files are appended with a unique time and date stamp it is therefore possible to create two or more files sharing the same name Note With Overlays 22 in Wavescan and Number of Samples 22 in Kinetics the overlaid data will always be saved automatically to the instrument s internal memory Warning when data is being written to the USB memory stick the LED will be lit DO NOT remove the memory stick at this stage otherwise data may become corrupted If you have completed your set of measurements exit the application which will close the file on the memory stick MANUAL SAVING If a method does not require sample data to be saved each time a measurement is taken it is possible to manually save sample data in one of the formats outlined above This procedure is described below Version 2 0 65 Wavescan After collecting all required sample measurements select Sanmnle Cis 2 SL Ha os FR save sample data from the options menu on the sample R measurement screen to display the dialogue box shown left The save location and filename are set by pressing the Save to and Sample Name boxes respectively If no Sample Name is entered the file will be titled Default Note Any sample data saved manually will override the auto save function EXPORTING DATA The BioDrop spectrophotometers allow users to recall saved sample data from the internal mem
32. ations BCA Bradford Lowry amp Biuret Protein Assays Determination of Protein Concentration using the BCA protein assay Determination of Protein Concentration using direct UV methods Protein UV Protein A280 SAVING amp PRINTING Saving Sample Data Internal USB USB csv Automatic Saving Manual Saving Version 2 0 19 19 19 19 20 21 Ze 253 25 27 EE 36 43 45 48 48 50 54 54 54 59 60 62 63 63 63 63 64 65 65 Exporting Data SAMPLE MANAGER Deleting data from the internal memory Accessing Sample Manager from the main screen Accessing Sample Manager from within an application Recalled files SAVING METHODS Methods saved to the internal memory Methods folder Renaming methods folder Locking saved methods Deleting saved methods Backing up method folders to USB Favourites folder Saving methods to USB PRINTING Built in Printer Print via computer PVC Automatic printing Manual printing Built in Printer Installation Built in Printer Paper Refill TECHNICAL SPECIFICATIONS TABLE OF ICONS GLOSSARY OF BOXES Version 2 0 66 66 67 68 68 69 70 70 71 71 71 74 72 Ia 73 73 73 73 74 74 75 77 79 80 85 HEALTH amp SAFETY Safety Conformance This equipment has been designed to conform to the following directives 2006 95 EC Low voltage equipment safety directive 2004 108 EC EMC directive 2002 96 EC EU Directive on Waste Electrical and Electronic Equipment WEEE
33. ber Samples of samples that will be measured during the 1 method Options are 1 2 or 3 Used in all applications to set the desired save USE location Only available locations are displayed Used in User Interface in Settings to set the time before the BioDrop screensaver will be displayed Screensaver Used by the Default Administrator in User Access to es set if user login will be displayed or not Version 2 0 10 00 T ext Entry Mode Sto Z Volume ml z 000 450 0 nm 550 0 nm Version 2 0 Used in all standard curve applications This is the number of standards that will be used to create the standard curve options are from 1 to 9 Numeric entry to 2 decimal places Used in all standard curve applications this is the concentration of the standard Used in User Interface in Settings to set the text entry mode used for alphanumeric text entry Used in applications where a concentration is the end result Units are entered via either alphanumeric entry or from a list of options Used in User Access when creating a new user Numeric entry to 3 decimal places this is used in the Cydye DNA application and is the volume of the probe in uL Numeric entry to 1 decimal place and is used in all fixed wavelength applications to determine the wavelength at which the measurement will be performed Numeric entry to 1 decimal place Used in the Cydye DNA application this is the wavelength at which the ab
34. button on the sample measurement screen This allows a method to be saved to a location specified by the user Save method parameters Accessed via the options button on the sample Save sample data measurement screen This allows sample data to be saved to a location specified by the user Accessed via the options button on the sample measurement screen Displays the sample data held in Sample Manager l i the either the internal memory or on a USB memory stick Accessed via instrument settings This displays instrument information such as product name serial number etc Instrument Information Accessed via instrument settings This allows the user to Instrument Settings set the default bandwidth save new baselines and view the date of the last service A e Lamp Settings Accessed via instrument settings Version 2 0 82 Save instrument options Auto print internal printer d Auto print USB Xenon lamp failed E Instrument busy E Printing to internal printer 9 m d Toggle view standard curve Replicates Take sample measurement Take reference measurement Version 2 0 Accessed via instrument settings This saves the instrument options Displayed on the status bar This indicates that the instrument will automatically print all sample data to the internal printer Displayed on the status bar This indicates that the instrument will automatically print all sample data via PV
35. cell density measurement English French English French Languages ENGS dan English German Spanish German Spanish panis TABLE OF ICONS ICON TITLE FUNCTION Back arrow Returns the user to the previous screen Forward arrow Advances the next screen in a sequence Displays the relevant options menu the exact content of the menu will depend upon the location Allows the user to navigate to the next page Allows the user to navigate to the previous page Used in the wavescan and kinetics applications to move the cursor left The position of the cursor and the Cursor left l corresponding x and y values are displayed above the scan Used in the wavescan and kinetics applications to move l cursor right The position of the cursor and the Cursor right l corresponding x and y values are displayed above the scan When used in the Cydye DNA application this toggles the data displayed between DNA and dye data Under Instrument Settings this will resets a value Deletes all saved data methods Delete all is a two stage Delete all process Delete Deletes the highlighted data method Delete is a two stage process Version 2 0 80 Open options menu Toggle data viewed reset enos entrees Thresholds Instrument Add linear section Method folder Rename method folder Used in Equation Editor This allows users to add thresholds pass fail limits to their results Used to confirm accept any cha
36. d here will be displayed in the Equations combo box on the Equation Builder screen as well the results screens Therefore any equation can be easily identified when using it in other equations Pressing this takes the user to the Equation Builder see below Any equation constructed in the Equation Builder will be displayed in this box Pressing this allows the user to enter units for the result of the equation using alphanumeric text entry If this column is left blank no units will be displayed alongside the result Pressing this deletes the row and removes the equation The Equation Builder allows the user to create any equations Variables required in the method Data is inputted as described below To allow data to be inserted or deleted the cursor can be moved left and right using the left and right arrows Data can be deleted using the delete icon and thresholds added using the thresholds icon see below 4 ak d Variables Constants Version 2 0 Pressing this displays a list that contains any variables added to the Variables table by the user Selecting the desired variable enters it into the equation Pressing this displays a list that contains any constants added to the Constants table by the user Selecting the desired constant enters it into the equation 39 Equations Sample Data Symbols Numbers Pressing this displays a list that contains any equations that have been created
37. d these into Trace Manager by pressing the Sample Manager icon bottom right corner If the files you require are not displayed on the screen you can scroll through the pages using the up and down arrows Pressing on the Sample ID and Date column headers will sort the files alphabetically and chronologically respectively Note If a USB memory stick is inserted it is possible to toggle between files stored on the internal and USB memories using the icon in the left hand corner The icon in the top right corner of the screen will display the memory that is currently in use stot Source Trace Owput Pa Tew Tsa tank aa beater a Tess ara eave Tanks 4th Derivative s Tees eae e tars emanced i CS Display E NEN W Emm mw X R 0 1 LET LE FROM WITHIN AN APPLICATION All recalled files will be displayed on the Trace Manager screen up to 8 The colour of the Slot number will be the colour of the trace when it is displayed on screen To toggle which files are displayed on the measurement screen press in the appropriate Display box up to 8 files can be displayed To select which files data will be displayed on the measurement screen press in the appropriate selected box only one file may be selected Press the forward arrow to view the overlaid data To overlay saved files with a live trace displayed Trace Manager can be accessed from within the application This procedure is
38. ders are detailed below NUCLEIC ACIDS DNA Utilises the absorbance measurements at 230 260 amp 280 nm with optional background correction to perform a concentration and purity check for DNA samples RNA Utilises the absorbance measurements at 230 260 amp 280 nm with optional background correction to perform a concentration and purity check for RNA samples Oligo Utilises the absorbance measurements at 230 260 amp 280 nm with optional background correction to perform a concentration and purity check for oligo samples Cydye DNA Measures the labelling efficiency of fluorescently labelled DNA probes to ensure that there is sufficient amount of each probe to give satisfactory signals The DNA yield is measured at 260 nm whilst the incorporation of the dyes is measured at the absorption maxima This method is also useful for measuring the yields and brightness of fluorescently labelled in situ hybridization probes TM Calc The Tm Calculation application calculates the theoretical melting point from the base sequence of a primer It is done using nearest neighbour thermodynamic data for each base in the nucleotide chain in relation to its neighbour PROTEIN BCA Quantitative determination of protein concentration utilising the absorbance measurement at 562 nm Bradford Quantitative determination of protein concentration utilising the absorbance measurement at 595 nm Lowry Quantitative determination of protein concentration utilising t
39. does not allow a user to delete sample data files from a USB memory stick this must be done using a PC Sample Manager allows the user to lock files saved to the internal memory to prevent the accidental deletion of files containing precious data To lock files highlight the required data and press the lock icon at the bottom of the screen Locked files are signified by the lock icon in the right hand column Once a file is locked selecting Delete or Delete All does not clear this data from the instruments internal memory To unlock a file highlight the appropriate locked data and press the lock icon at the bottom of the screen Note As sample data files saved to a USB memory stick must be deleted using a PC it is not possible to lock USB sample data using Sample Manager To exit from Sample Manager press the Exit icon Version 2 0 67 ACCESSING SAMPLE MANAGER FROM THE MAIN SCREEN de i Applications Favourites Methods Ft FE GD Life Science Sample Manager Settings gB g c Switch ser Sample Manager page 1 of 2 4 a CEC mm 2010 01 26 13 27 05 NA DNA 25 4 ES cs 8 4 xXx 2 amp leje e jf When accessed from the main screen Sample Manager will display all files held on the internal memory or USB memory stick and allows the user to lock and delete files saved to the internal memory As Sample Manager accessed from the main screen allows users to delete files from the i
40. down menu of the Pathlength list We recommended the use of the BioDrop 500 for the highest sensitivity and BioDrop 125 and uLite sample port analysis 0 5mm pathlength for low volume samples Pathlength factors are pre programmed in the software for quick calculations For example if measuring dsDNA in a BioDrop 125 the calculation would be as follows Concentration A260 x 50 ug ml x 80 If measuring dsDNA in the BioDrop 500 the calculation would be Concentration A260 x 50 ug ml x 20 NUCLEIC ACID PURITY CHECKS e Nucleic acids extracted from cells are accompanied by proteins and extensive purification is required to separate these protein impurities The ratio of A260 A280 gives an indication of a sample s purity with pure DNA and RNA preparations typically having ratios of 21 8 and 22 0 respectively Deviations from these values indicate the presence of impurities but care must be taken when interpreting results e Concentration also affects both the A260 and A280 readings If a solution is too dilute the readings may be at the instrument s detection limit and results may vary as there is less distinction of the A260 peak and A280 slope from the background absorbance For accurate measurements A260 should always be greater than 0 1 e Elevated A230 values can also indicate the presence of impurities 230 nm is near the absorbance maximum of peptide bonds and also indicates buffer contamination since EDTA and other buffer salts absorb
41. e reference suffices for standard curve creation o 5 An A ED s 30 Insufficient data Continue recording all standards replicates until the oO 8 8 standard curve has been completed To repeat any standard measurements simply press the desired result insert the correct standard and press take measurement Note After all replicates have been taken for a particular standard pressing the replicates icon takes the user to the next standard that was specified in the method Standard Curve HET To ignore any outlying standard measurements press the 0 050 A 0 100 tick in the appropriate row to toggle it to a cross Any ignored measurement will be automatically removed from the standard curve These can be reinstated by pressing the Cross o 1 2 3 4 y 0 04924 R 0 9725 gt 88 Version 2 0 34 TAKING A MEASUREMENT After the standard curve has been collected press the forward arrow to proceed to the sample measurement screen 8 B Standard Curve Sample Screen B To perform a measurement insert the cuvette or load Sample directly onto the pLite sample port containing the reference solution in the cuvette holder and press the take reference button Remove and replace with a cuvette containing the sample and press the take measurement 0 500 4 3 mg 100ml button A single reference suffices for subsequent analyses in the same series To view the standard curve whilst on t
42. ed from the latter summation Total Extinction Coefficient E 2 2x aTable base_type base n base n 1 tTable base type base n CONVERSION FACTOR The Conversion Factor is given by Molecular weight agcpr 2 EABCDE where E ABCDE 2 X EAB EBC ECD EDE EB EC ED e The molecular weight MW of a DNA oligonucleotide is calculated from MW g mole dA x 312 2 dC x 288 2 dG x 328 2 dT x 303 2 MWcounter ion x length of oligo in bases for RNA oligonucleotide dT x 303 2 is replaced by dU x 298 2 The MW calculated using this equation must be adjusted for the contribution of the atoms at the 5 and 3 ends of the oligo For phosphorylated oligos Add 17 2 x MW of the counter ion For non phosphorylated oligos Subtract 61 MW of the counter ion The MW g mole of the most common oligo counter ions are Na sodium 23 0 K potassium 39 1 TEA triethylammonium 102 2 Other Defaults to 1 0 variable 0 1 999 9 Calculated molecular weight a weight is added for each base looked up from a table The weight of the counter ion is added for every base from a small table for the known ions If phosphorylated then the system adds 17 0 plus two counter ions otherwise it subtracts 61 0 and one ion Theoretical Absorbance for each adjacent pair of bases nearest neighbours a weight is accumulated using a table For each internal base a weight is subtracted using another
43. et the sequence of bases The bases A C G T can be added in DNA mode and the bases A C G U can be added in RNA mode E c al nal Bases are grouped in threes to improve readability Used in Tm calculation to toggle between DNA and AAEE DNA Brightness Used in User Interface in Settings to set the brightness of the screen Version 2 0 85 Buffer Molarity 0 700 Standards Correction Factor 0 060 Counter lon Custom Oye Name 1 000 Version 2 0 Numeric entry used in Tm calculation only Buffer molarity buffer molarity total molarity of salt moles L Used in all standard curve applications to set the method used to collect the standard curve Options are for Standards or Manual Set by numeric entry used in the Cydye DNA application only This is the correction factor applied to the absorbance of the dye at a specified wavelength Used in Tm calculation only this allows the user to add the type of counter ion used The options are sodium Na potassium K triethylammonium TEA or other If other is selected the molecular weight of this counter ion must be added using Other MW Used in all standard curve applications this is the curve fit that will be applied to the standards absorbance values Options are Zero Regression Regression Interpolation and Cubic Spline Alphanumeric entry for custom dye name used in Cydye DNA only Numeric entry This is the delay required before
44. g alphanumeric entry a 4 digit password and assigned to one of three user Password d groups depending on the access level they require The table below outlines the features each user group can access X User Run Applications amp Save Sample Delete Sample Data from the Save Access Access User Group Saved Methods Data instrument s memory Methods Settings Menu Settings EARN Editing a user To edit a user s details highlight the desired user and select Edit user on the touch screen This allows the username password and user group to be edited updated as above Deleting a user To delete a user from the instrument highlight the desired user and press the Add user icon Any methods or data created by this user will not be deleted Note It is not possible to delete the default administrator account Version 2 0 19 Editing User Access To disable user logins and user access highlight the default E 4 J H administrator account and press Edit User to display the screen left Note With Show Login set to No the instrument will not prompt for User Log on at start up the Switch User icon will not be displayed on the main screen and the instrument will always be in Administrator mode PERFORMING A MEASUREMENT BIODROP SPECTROPHOTOMETERS The BioDrop spectrophotometers are a split beam UV visible spectrophotometer that contains a single cuvette holder for both reference and sample me
45. ges exist within the power supply unit and the Xenon lamp housing Repair and maintenance should only be carried out by individuals trained to work on these instruments Version 2 0 1 Version 2 0 There are no bio hazardous materials within the unit however this unit may be exposed to bio hazardous samples during normal laboratory use We recommend the following decontamination procedures of this instrument to protect users remove cuvettes and cuvette holders and wash with appropriate disinfectant for the bio hazard in question rinsed with distilled water and then allowed to dry The exterior may be wiped with a suitable disinfectant cleaning wipe In addition we recommend the following e Include an appropriate decontamination certificate for equipment returned for repair Ensure that the operator of the equipment is provided with a safe working environment Use store and dispose of any chemicals in accordance with manufacturer s guidelines and local safety regulations Provide suitable ventilation when working with volatile solvents or toxic substances Dispose of solvents and chemicals that may be classed as hazardous waste in accordance with local regulatory practice Determine if personal protective equipment PPE is required for handling laboratory samples All models can be connected to and operated from a PC Those without a user interface cannot be operated without a PC To preserve the integrity of the measuring equipment i
46. he 8546 2 ec T Lite sample port and press the take measurement button 34144 A single reference suffices for subsequent analyses in the x 8 8 same series SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 53 PROTEIN APPLICATIONS The BioDrop spectrophotometers contain dedicated methods for both colorimetric protein assays and direct UV measurements BCA BRADFORD LOWRY amp BIURET PROTEIN ASSAYS The BCA Bradford Lowry and Biuret protein assays are well established spectrophotometric methods for determining the amount of protein in a sample The exact choice of the assay depends upon the concentration of protein being measured and the detergents reducing agents used in purification Detailed protocols are supplied with all assay kits and should be followed closely to ensure accurate results are obtained An outline of the protein assays offered by the BioDrop TOUCH is provided below Bradford method Quantifies the binding of the dye Coomassie Brilliant Blue to an unknown protein and compares this binding to that of different known concentrations of a standard protein at 595 nm The standard protein is usually bovine serum albumin BSA Biuret method Depends on reaction between CU ions and amino acid residues in an alkali solution The resulting copper complex absorbs light at 546 nm BCA method Depends on reaction between Cu ions and amino acid res
47. he absorbance measurement at 750 nm Version 2 0 43 Biuret Protein UV Protein A280 Version 2 0 Quantitative determination of protein concentration utilising the absorbance measurement at 546 nm Direct UV determination of protein concentration at 280 nm using the Christian Warburg calculation Direct UV determination of protein concentration using BSA IgG Lysozyme Molar Extinction Mass Extinction or E196 calculations 44 NUCLEIC ACID APPLICATIONS DNA RNA amp Oligo Nucleic acids can be quantified at 260 nm because it is well established that solutions of DNA and RNA in 10 mm pathlength cuvettes with an optical density absorbance of 1 0 have concentrations of 50 ug ml and 40 ug ml respectively Oligonucleotides typically have a factor of 33 ug ml although this does vary with base composition and can be calculated if the base sequence is known Concentration A260 x Factor BioDrop spectrophotometers use the default factors 50 40 and 33 for DNA RNA and oligonucleotides respectively Compensation for dilution and pathlength can also be entered The BioDrop TOUCH and the BioDrop Duo is designed for use with the BioDrop CUVETTES The BioDrop CUVETTE is available in two pathlength configurations the BioDrop 125 has a pathlength of 0 125 mm and the BioDrop 500 has a pathlength of 0 5 mm The BioDrop uLite and Duo harbour a direct microvolume sample port with a pathlength of 0 5mm which can be selected from the drop
48. he following parameters 60 C for 15 minutes 37 C for 30 minutes or room temperature from 2 hours to overnight 3 If required allow the tubes to cool to room temperature SAMPLE PREPARATION 1 Prepare the unknown samples as described above ensuring that the final volume is 0 1 ml Add 2 0 ml of the BCA working reagent to each sample vortex gently and incubate using one of the following parameters 60 C for 15 minutes 37 C for 30 minutes or room temperature from 2 hours to overnight 3 If required allow the tubes to cool to room temperature Version 2 0 55 CREATING A STANDARD CURVE BCA Instrument Par amebers For BCA measurements Wavelength is set to 562 0 nm Integration Time and Sample ID can be set as you wish Integeatlon T ame You may advance to the next screen at any time by pressing the forward arrow and return to the previous screen by pressing the back arrow Set Calibration to Standards Curve Fit to Zero Regression and Calibration enter Units of mg ml The number of standards and replicates Standards Zero Regression can be set as you wish for optimum accuracy it is recommended Standards that the number of standards is 24 and replicates is gt 1 Replicates Note With Calibration set to Standards the user is required to prepare and measure standards with Calibration set to Manual the user inputs both the standard concentrations and absorbances BCA Standards 0 200 0 800 0 400 1 000
49. he sample measurement screen simply press the View Curve icon that appears under the options menu Note Saving the method using the Save Method icon that appears on the options menu will save both the method parameters and the standard curve Recalling a method containing method parameters and standard curve allows the user to measure samples directly SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 35 Equation Editor The Equation Editor application allows users to create their own unique methods that include calculations and thresholds Examples of methods that can be created using Equation Editor include percentage strength calculations and olive oil and chlorophyll analyses GETTING STARTED The use of Equation Editor is outlined below MEASUREMENT PARAMETERS Ecguation E daar Instrument Parameters T MWegration Time The first screen of Equation Editor allows the user to set the measurement parameters that will be used for all subsequent measurements Integration Time and Mode are used as in all other applications The use of Prompt between is described below Prompt between A off The instrument will measure wavelength 1 measure wavelength 2 measure wavelength 3 etc and then perform any calculations Prompt between A on The instrument will measure wavelength 1 prompt measure wavelength 2 prompt measure wavelength 3 etc and then pe
50. idues In addition this method combines this reaction with the enhancement of Cu ion detection using bicinchoninic acid BCA as a ligand giving an absorbance maximum at 562 nm The BCA process is less sensitive to the presence of detergents used to break down cell walls Lowry method Depends on quantifying the colour obtained from the reaction of Folin Ciocalteu phenol reagent with the Tyrosyl residues of an unknown protein and comparing with those derived from a standard curve of a standard protein at 750 nm usually BSA DETERMINATION OF PROTEIN CONCENTRATION USING THE BICINCHONINIC ACID BCA PROTEIN ASSAY The principle of the bicinchoninic acid BCA protein assay relies on the formation of a Cu protein complex under alkaline conditions followed by reduction of the Cu to Cu The amount of reduction is proportional to the amount of protein present BCA forms a purple blue complex with CU in alkaline environments thus providing a basis to monitor the reduction of alkaline Cu by proteins The BCA assay can be used to quantify proteins in the concentration range 0 2 to 1 0 mg ml It is compatible with many detergents but not compatible with reducing agents such as dithiothreitol above 1 mM GETTING STARTED It is always advisable to prepare the standard in the same buffer as the sample to minimise any interference effects BCA assays are routinely performed at 37 C Colour development begins Version 2 0 54 immediately and ca
51. in this method Selecting the desired equation enters it into the equation Pressing this displays a list that contains all of the readings specified by the user in the Sample Measurement table Selecting the desired sample data enters it into the equation Pressing this displays a list containing mathematical symbols and the logic gates AND and OR Selecting the desired symbol enters it into the equation Pressing this produces the number entry box that allows the user to directly input numbers into the equation Note All of the data above appears in the lists as it was inputted in the appropriate table After the equation has been inputted the user has two options If the result is to be viewed as a number press the back arrow to return to the Equation Viewer screen If the result is to be viewed with a user specified pass fail limit press Thresholds to set appropriate thresholds for the measurement Equation E ditor L T aa E The first thresholds screen allows the user to input how many thresholds are required for a result vau Name With Thresholds set to 3 the screen will display the table Value Name Version 2 0 layout shown left Setting Thresholds to 2 and 1 will reduce the number of values you can input to 2 and 1 respectively Pressing this produces the number entry box that allows the user to directly input numbers for threshold values Pressing this allows the user to enter the text
52. ing one of the existing co Date Time Right click in the appropriate cell and select Format Cells from the list under Category select Date or Time and the desired format from the list on the right hand side see below and select ok Version 2 0 64 Format Cells Number Alignment Font Border Fill Protection Category General Sample Number 15 04 2010 Currency fos ER Type i Time Percentage 1 eia E I Fraction Scientific Text Special Custom Locale location English U K Date Formats display date and time serial numbers as date values Date Formats that begin with an asterisk respond to changes in regional date and time settings that are specified For the operating system Formats without an asterisk are not affected by operating system settings AUTOMATIC SAVING Single Wavelength The option to save sample data automatically is set under method parameters With Auto Save set to on the save location can be set to Internal USB or USB CSV the USB options are only available if a USB memory stick is inserted The filename given to an automatically saved file will be either the Sample Seed entered in the method parameters or if the user chooses not to enter a Sample Seed Default The BioDrop TOUCH will only save one Default file per application subsequent saves of files without a sample seed will overwrite the previous default file As sample data is saved when the user exits the applic
53. ions menu USB in the methods folder to allow the user to backup methods to a USB memory stick Displayed under User Access this allows anyone with Add user Administrator privileges to add another user to the instrument Displayed under User Access this allows anyone with Delete user Administrator privileges to delete users from the instrument Displayed under User Access this allows anyone with Edit user Administrator privileges to edit currently users parameters sod Used in the wavescan and kinetics applications This allows the user to zoom into a specific region of a scan Version 2 0 84 Ren E Used in the wavescan and kinetics applications This Zoom out allows the user to zoom out and return to the original scan GLOSSARY OF BOXES Toggles between on and off Used in all applications to set whether sample data is printed automatically or not Toggles between on and off Used in all applications Dn to set whether sample data is saved automatically or not Can be toggled on and off Used in nucleic acid and protein measurements to subtract the absorbance value at 320 nm This is done to allow for the effects of turbidity high absorbance buffer solutions and On the use of reduced aperture cuvettes Set by numeric entry Used in Cydye DNA measurements only and enables the user to specify the wavelength of background correction 320 0 nm Base Sequence Used in Tm calculation to s
54. is inputted as Nose 100 sample x described below Before any data is inputted Variable Name a a will read Not set and will not appear in the Variables list on Morc sme sawe the Equation Builder em T cane Variable Name Pressing this allows the user to input an alphanumeric name for the variable factor Default Selecting this produces the number entry box that allows the user to input the default variable factor Default values can be edited during a measurement Units Selecting this allows the user to enter units for the variable factor using alphanumeric text entry If this column is left blank no units will be displayed on exported or printed data Version 2 0 38 Change Each Name Equation Units Del Pressing this toggles between sample and batch When set to sample the method will prompt for a variable to be entered before each sample measurement When set to batch the method will prompt for a variable to be entered at the start of each sample batch Equation E ditor Equation Viewer The Equation Viewer screen provides an overview of any equations created as well as allowing the user to create new or edit existing equations Data is inputted as described below Before any data is inputted Name will read Not set and will not appear on the results screen Pressing this allows the user to input a unique alphanumeric name for the equation The names entere
55. lope and is the value that will be multiplied by the Factor to give the Facto Units O Result on the sample measurement screen Units are entered using alphanumeric text entry and will appear on any printed or exported data Y min and Y max are what is E displayed during the measurement the y axis auto scales upon completion Set the outputs required in your method For more information see the section Saving and Printing To perform a measurement insert a cuvette or load directly onto the uLite sample port containing the reference solution in the cuvette holder and press the reference button Remove and replace with a cuvette containing the sample or load sample directly onto the uLite sample port 0 50 suffices for subsequent analyses in the same series ER E E R R E RC and press the take measurement button A single reference a amp A measurement can be stopped at any time by pressing the Stop button at the bottom of the screen All data collected to this point will be displayed on screen and can be saved The data displayed in the table below the scan refers to the full measurement range To obtain data for a specific 28 section it is necessary to add sections this is done as follows Set the cursor to the desired start position by either pressing on the scan or using the cursors select tO from the options menu set the cursor to the desired end position and select t1 from the options
56. matically depending on the units selected i e for units of ug ml the default factor will be 50 00 If the Factor required differs from the default value this can be edited using numeric entry The Sample Seed entered under Sample will be the filename of any saved file Version 2 0 46 forward arrow and return to the previous screen by pressing the o oA Internal Printer Internal back arrow Set the outputs required in your method For more information see the section Saving and Printing TAKING A MEASUREMENT To perform a measurement insert a cuvette or load directly onto the uLite sample port containing the reference solution in the cuvette holder and press the reference icon Remove and replace with a cuvette MMC MEER containing the sample or load sample directly onto the ee MA uLite sample port and press the take measurement icon A single reference suffices for subsequent analyses in the same series If Background is set to On the A320 result will be included in the left hand column and automatically subtracted from the displayed A230 A260 A280 A260 A230 A260 A280 results A scan of the most recently run sample can be viewed by pressing the View Scan icon in the options menu Note When saving sample data scan files will not be saved The Wavescan application should be used to save scans of ug ml nucleic acid samples aa 240 260 280 300 390 L X g A SAVING amp PRINTING For details
57. ment Toggles between 1 and 2 Used in Cydye DNA application only to set the number of dyes used in the measurement Numeric entry This option is only used if the counter ion type in the Tm calculation is set to Other Used in User Access to set a password for new users Used in the nucleic acid applications Protein A280 and Protein UV This is the pathlength of the cuvette used in the measurement Options are for 10mm 5mm 2mm 1mm BioDrop500 BioDrop125 and uLite 0 5 mm 88 Toggles between yes and no Used in Tm calculation to set if the sample to be measured is phosphorylated or not Numeric entry to 3 decimal places Used in Tm 1 000 calculation to sets the primer concentration in pmole mL Printto Used in all applications to set the desired print location Only available printers are displayed Toggles between On and Off used in Equation Editor only With Prompt on the measurement will p iE cj proceed as follows measure wavelength 1 prompt for sample measure wavelength 2 prompt for sample etc Used in all standard curve applications This is the number of times a standard measurement is 3 repeated before the mean of these values is plotted on the standard curve Options are off 1 measurement 2 or 3 sample Overlays Used in wavescan measurements this determines how many samples will be overlaid on the graph Options are off 2 to 8 Used in kinetic measurements this sets the num
58. mes are entered by pressing on the desired row and entering the standard name using alphanumeric text entry Standard measurements can be made for any measurements specified in the Samples table Equation Editor Constant Factor Specification Consan Name Vale Unts De The Constant Factor Specification screen is used to declare Z foe E any constants used in the equation Data is inputted as Mem f o Notset 19 x described below Before any data is inputted Constant LT seco Name will read Not set and will not appear in the Mem seco i Nose o s Constants list on the Equation Builder Ma fo Mem fo fi Constant Name Pressing this allows the user to input an alohanumeric name for the constant Value Pressing this produces the number entry box that allows the user to input the value of the constant Units Pressing this allows the user to enter units for the constant using alphanumeric text entry If this column is left blank no units will be displayed on exported or printed data Del Pressing this deletes the row If the constant is used in an equation this will also be deleted Equation E ditor Variable Factor Specification Variable Name Default Units Change On Det ose 190 sawe The Variable Factor Specification screen is used to declare hm noo ew ub Nese vw sme x any variables used in the equation Data
59. ms Ta aaas iow Lew 20tarat 26 132860 the left hand corner of the screen The location of the _L Ee displayed data will be indicated by the icon in the top right hand corner Version 2 0 66 Sample Manager has been designed to make finding saved files as simple as possible Therefore it is possible to arrange files alphabetically by application or by date time saved by pressing the column headers Sample ID Application and Date respectively If there are too many saved data files to fit on a single screen this is signified at the top of the screen e g Page 1 of 2 Scrolling through the screens is achieved using the up and down arrows at the bottom of the screen Note Sample Manager can only display the first 100 sample data files if the internal memory or USB stick contains gt 100 files these can be viewed be deleting or moving USB only unwanted data DELETING DATA FROM THE INTERNAL MEMORY To ensure that the internal memory of the instrument does not contain too many unwanted data files Sample Manager allows you to delete files This can be done in one of three ways Deleting a single file Highlight the file for deletion and press the delete button Deleting multiple files Highlight multiple files and press the delete button Deleting all files Press the Delete all icon at the bottom of the screen Note It is only possible to delete data using Sample Manager accessed from the main screen Sample Manager
60. n be accelerated by incubation at higher temperatures Higher temperatures and or longer incubation times can be used for increased sensitivity MATERIALS REQUIRED Bicinchoninic Acid Kit for Protein Determination Suitable tubes with caps to hold and mix 2 1 ml samples and to heat at up to 60 C Plastic disposable cuvettes Standard protein solution of known concentration 1 mg ml Incubator or block heater to heat sample tubes PREPARATION OF THE BCA WORKING REAGENT BCA reagents A and B are available commercially from a number of different sources Instructions given here are for the kit supplied by Sigma Aldrich other methods will be similar Always refer to the manufacturer s instructions 1 Mix 50 parts of Reagent A a solution containing bicinchoninic acid sodium carbonate sodium tartrate and sodium bicarbonate in 0 1N NaOH pH 11 25 with 1 part of Reagent B 4 w v CuSO 5H O preparing sufficient reagent for all the standards and samples 2ml of working reagent is required for each sample 2 Mixuntil the solution is a uniform light green colour The solution is stable for 1 day STANDARD PREPARATION 1 Prepare a series of protein standards ranging in concentration from 0 2 to 1 0 mg ml such that the final volume for the assay is 0 1 ml The BioDrop spectrophotometers can measure up to 9 standards and up to 3 replicates 2 Add 2 0 ml of the BCA working reagent to each standard vortex gently and incubate using one of t
61. n course Options are Off Coarse Sensitive or Custom when custom is selected the minimum peak height and width must be entered Toggles between wavelength and absorbance used in wavescan measurements only This determines how features will be ordered in the peak valley table below the scan Toggles between peaks and valleys used in wavescan measurements only This determines what feature type will be detected Used in User Access to set the group a user will belong to and what access they will be granted 87 Integration Time 1 000 Maz Wavelength Min wavelength Absonbance Mucleic Acids d DNA 2Z60nm Number of Dyes Other Wiw 1 000 1000 Version 2 0 Used in all applications This is the duration the instrument will take a reading at an individual wavelength The longer the integration time the greater the signal to noise ratio and the greater the accuracy Numeric entry This is the interval at which serial kinetics readings will be taken Numeric entry This is the upper limit of a wavescan measurement Numeric entry This is the lower limit of a wavescan measurement Note that when using the BioDrop TOUCH the max wavelength must always be greater than the min wavelength by at least the step value Used in the Single Wavelength Kinetics and Protein A280 applications to set the required measurement mode Used in Cydye DNA application only this sets the nucleic acid used in the measure
62. nd solvents may be classified as hazardous or bio hazardous waste The disposal of such substances must be carried out in accordance with local regulatory practice Performance Validation Good laboratory practice requires that the unit is periodically checked for optical performance e Switch on validation tests When the unit is powered up it performs wavelength accuracy and lamp energy tests e Periodically wavelength stray light and absorbance accuracy should be tested to ensure the unit is performing to specification Deterioration in performance may indicate that the instrument requires service Performance validation can be performed using reference materials User Maintenance e There are no user serviceable parts in this instrument e TO prevent cross contamination and protect users from occupationally acquired infections keep the unit clean and free from contaminates o Cuvette holders and accessories should be removed and cleaned with commercially available cleaning solution or dilute detergent followed by a thorough rinse in deionised water Allow to dry thoroughly before use o Casework and the sample compartment may be wiped down with commercially available disinfectant wipes o Periodically validate the optical performance and refer the instrument for regular servicing and calibration If the equipment is operated in a manner not specified then the protection provided by the equipment may be impaired and the instrument wa
63. ndard measurements press the tick 0 100 next in the appropriate row to toggle it to a cross Any ignored 4 000 measurement will be automatically removed from the standard curve These can be reinstated by pressing the cross y 0 04924 R 0 3725 gt 8 8 Note Pressing the save method icon before any standards have been measured will save the method parameters only Recalling a method containing method parameters only will require the user to construct a standard curve before measuring samples Version 2 0 57 TAKING A MEASUREMENT BCA Sample Screen To perform a measurement insert the cuvette containing Sel the reference solution in the cuvette holder and press the e take reference icon Remove and replace with a cuvette containing the sample and press the take measurement 0 367 7 icon A single reference suffices for subsequent analyses in mg ml the same series To view the standard curve whilst on the sample measurement screen simply press the View Curve icon that appears under the options menu Note Saving the method using the Save Method icon that appears on the options menu will save both the method parameters and the standard curve Recalling a method containing method parameters and standard curve allows the user to measure samples directly SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section Version 2 0 58 DETERMINATI
64. nges Exits from an application or screen If exit is selected without saving any changes will be lost Locks sample data file method folder against accidental deletion Unlocks a locked method folder Used in Sample Manager to access sample data files stored on the instrument s internal memory or to indicate that the data being displayed is from the internal memory Used in the kinetics applications to view a line of best fit on the scan Used in kinetics applications to view data in a specific section It is possible to add tO through to t7 Methods saved internally can be stored in one of nine method folders each capable of storing up to nine individual methods Accessed via the options menu on the methods screen this allows the method folder to be renamed Version 2 0 81 Used in the nucleic acid applications DNA RNA and Oligo this allows the user to view a survey scan of the last sample run in the region 220 320 nm Toggle auto print on Accessed via the options button on the sample screen or off Pressing this button toggles auto print on and off Accessed via the options button on the sample View method i measurement screen Pressing this button takes the user parameters back to the method parameters Toggle view scan on or off 0 Accessed via the options button on the sample Print data measurement screen Pressing this button prints the sample data Accessed via the options
65. ngth setting of 0 5mm H and can be selected from the drop down menu under Pathlength units H Factor o 0 j o y Version 2 0 22 TAKING A MEASUREMENT To perform a measurement insert a cuvette containing the reference solution in the cuvette holder for uLite and Duo Same load reference directly on the wLite sample port and press the reference button Remove and replace with a cuvette containing the sample For the uLite sample port wipe away 0 550 the reference with a lint free cloth and load the sample directly on the port When the sample is loaded press the Take Measurement button A single reference suffices for subsequent analyses in the same series SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section CONCENTRATION VIA FACTOR This mode within the Single Wavelength application makes simple concentration measurements on samples Concentration is obtained by multiplying the measured absorbance at a specific wavelength by a factor The factor may be known in advance or may be calculated by the instrument by measuring a standard of known concentration Examples of concentration measurements include DNA or protein MEASUREMENT PARAMETERS From the main screen of the BioDrop spectrophotometer select Applications followed by Single Wavelength to display the screen below Set Mode to Concentration Wavelength and Integration avelength
66. nstrument s internal memory this option is disabled for Limited users To allow post scan manipulation of saved wavescan and kinetics data files loaded from Sample Manager are loaded directly into Trace Manager see Trace Manager section for details Note With large numbers of files held on the internal memory there may be a short delay before Sample Manager opens ACCESSING SAMPLE MANAGER FROM WITHIN AN APPLICATION e Sample Manager Page 1 of 1 Samples Appication Dae nate sae wave xorosror ose SilI e When accessed from within an application Sample Manager will only display files belonging to that specific application and only allows users to recall saved data and lock files Version 2 0 68 RECALLED FILES When recalled sample data files will display the first sample recorded in a measurement To access all sample data within a recalled file press the Sample box to display a list of all samples contained within the file Pressing on the desired file will populate the boxes on the sample measurement screen with the saved data Choosing to measure another sample with an old sample s data displayed simply updates the sample measurement screen and the appropriate boxes Single Wavelength Test 8 Test 9 Test 10 Test 11 Test 12 Test 13 Test 14 Note Wavescan and kinetics sample data is recalled using Trace Manager For details see the Trace Manager section for details Version 2 0 69 SAVING
67. od e Where relevant set up the application parameters for the sample e Select the correct type It is important to use cuvettes with the correct parameters Most samples are measured using a standard 10mm path length cuvette Special cuvettes and accessories are available for larger or smaller path lengths and sample volumes The BioDrop CUVETTE is an example of a specialized micro volume cuvette which can be used with the spectrophotometer It is important to use cuvettes of the correct type Plastic used in many cuvettes absorb UV light and thus are not suitable for UV sample measurement Cuvettes used for measurement should be free from dust residue or scratches e Before preparing samples and sample reference blanks familiarise yourself with hazards arising from handling the sample materials and where necessary observe local regulatory practice personnel protection equipment and measures designed to ensure your safety e Prepare the sample blanks reference in the same solution used to dissolve the sample e Prepare the sample solutions Version 2 0 7 When placing the cuvette in the equipment ensure the cuvette is orientated so that the light energy will pass through the cuvette Post Run procedures e Empty cuvette and rinse with deionised water e Clean cuvettes periodically with commercially available cleaning solution or dilute detergent solution followed by several thorough rinses in deionised water e Note that some samples a
68. options menu the left Wavelen S hand icon and selecting the desired file Kinetics Standard Curve Note Locked methods must be unlocked to allow deletion BACKING UP METHOD FOLDERS TO USB amp L k uM Pnn raer With a USB stick inserted it is possible to use the USB icon on fi f f the options menu the right hand icon to Methods 4 Methods 5 Methadz 6 Methods 7 ux Methods 9 Backup Folder Copies all methods from a specified folder to la d a USB memory stick Restore Folder Copies a backed up method folder from the USB memory stick to the internal memory l Backup All Folders Copies all method folders from the Backup Folder internal memory to a USB memory stick Restore Folder Backup All Folders Restore All Folders Copies all backed up method folders danda from the USB memory stick to the internal memory FAVOURITES FOLDER H M Single Single Wave Wavescan The Favourites folder is capable of storing up to 9 user Wavelen LS Pd defined methods Methods stored in the Favourites folder Kinetics Standard Curve can be locked and deleted as described above Version 2 0 72 SAVING METHODS TO USB To save files to a USB memory stick follow the procedure described above and select USB in the Folder box The USB option will only appear in the list if a USB memory stick is inserted Method Name Methods saved to a USB memory stick will appear in the x BioDrop Methods folder in the roo
69. or DNA Quantity the relevant nucleic acid can be inputted A custom factor can be entered by selecting Custom in Nucleic Acids LDribation Facies factor and volume of the sample in ul All of these will be This parameters screen allows the user to set the Rmn pathlength of the cuvette being used whether background RS correction is required and at what wavelength the dilution _ we used in the calculations The Sample Seed entered under Back armis ageleruth Volume ill g Sample will the filename of any saved file LRN Version 2 0 48 CyD ye DNA Prntto Saveto ET J Set the outputs required in your method For more nternal Printer Internal information see the section Saving and Printing CyDye DNA A230 oora To perform a measurement insert a cuvette or load directly azeo omsa onto the uLite sample port containing the reference solution DNA Concentration Ame oo accen in the cuvette holder and press the reference button Remove nnm and replace with a cuvette containing the sample or load Azeo A2s0 1000 EPUM sample directly onto the uLite sample port and press the take A260 A280 1 800 O measurement button A single reference suffices for X 8 subsequent analyses in the same series CyDye DNA Sample s If Background Correction is set to On the Background Wavelength set in the method will be included in the left
70. ory or a USB memory stick and save this in another format This is done as follows Recall saved data using Sample Manager and press the save sample button on the options menu to display the save sample dialogue box Set the desired save location and filename using the Save to and Sample Name boxes respectively and press the tick to confirm the data export SAMPLE MANAGER Sample Manager is the application used by the BioDrop spectrophotometers for saving and recalling data from both the instrument s internal memory and the instrument s USB format Sample Manager can be accessed from either the main screen pressing Sample Manager below left or from within an application using the Sample Manager icon on the options menu below right Libra 550 de i O e ir d Life Science Sample Manager Settinas m R 89 F p Logout Switch Liser To recall a saved file highlight the desired file and press Sample Manager page 1 of 2 Sample id Application Dae TA the Sample Manager icon in the right hand corner of the A280 Pian azn 2010701726 1331 05 screen Data will be displayed on the Sample Measurement ane 460 arae wave 2010701726 162 60 m sca oa Iae Screen see Recalled Files below sears Bader woven V NM Ge Dye DNA 2010701726 152705 B With a USB memory stick inserted it is possible to toggle DN ona 200 0 29 13250 between the internal and USB memories using the icon in ai
71. ows the user to manually save sample data to a Save data M specified location Allows the user to save the current method Save method parameters to the internal memory or a USB stick Rmo om Prints the sample data from the specified printer Toggles auto print on and off green surround i Auto print on LP Sample Manager Accesses Sample Manager Version 2 0 Bi 13 da Accesses Trace Manager wavescan and kinetics Trace Manager only First time powered on The first time the BioDrop spectrophotometer is powered on the user will be prompted to set their regional setting preferences for language and local date time REGIONAL TT The BioDrop spectrophotometer will arrive with the language set to English This can be changed by pressing the Spanien To save any alterations press the tick to exit without saving Language box the options are English French German and press the cross The BioDrop spectrophotometer will arrive with the UK time and date set This can be changed by pressing Date and Time After the desired date and time have been entered select the tick to save and exit or the cross to exit without saving X Version 2 0 14 TYPES OF BOXES The BioDrop spectrophotometer uses different kinds of boxes for parameter selection and entry these include Alphanumeric Text Entry Sample Seed The alphanumeric text entry box allows the user to enter letters numbers and
72. reduce noise and smooth the data Enhanced Enhances features sharpening peaks and valleys Kinetics post scan manipulations are Sample Data Displays the raw kinetics data this is the default option Low Applies a low level of smoothing to the data Medium Applies a medium level of smoothing to the data High Applies a high level of smoothing to the data amp Wavescan After the manipulations and display options have been set as required press the forward arrow in the right corner to display the recalled data on the sample measurement screen Note For wavescan and serial kinetic measurements with overlays set to gt 1 and parallel kinetic measurements data will be automatically saved into the instrument s internal memory and displayed in Trace Manager To ensure the optimum performance of the instrument it is recommended that unwanted files are deleted from the internal memory at regular intervals see Sample Manager deleting files from the internal memory Version 2 0 32 STANDARD CURVE The construction of a multi point calibration curve from standards of known concentration to quantify unknown samples is a fundamental use of a spectrophotometer The BioDrop spectrophotometers have the advantage of being able to store calibration curves with a method Each calibration curve can be created using up to 9 standards with each standard measurement being made of up to 3 replicates CREATING A STANDARD CURVE Hamdard Cun
73. required for Limited users as they do not have the ability to access Sample Manager on the main screen Wavescan A 450 0nm Abs 0 000 Version 2 0 Trace Manager can be accessed from the Wavescan and Kinetics measurement screens using the Trace Manager icon on the options menu 30 Trace Manager Sample Manager page 1 of 4 aa icon Ja ewm Waveseon aroraa rem avesar zorezrosos52 o Gi reso wavesan 20100208 003232 B rese Wavesean EIR rese wueesc EID rani averen anora oaza R aroro oaz rari averen anora oaza E X S Z 5 When accessed with no overlays displayed Trace Manager will be empty Files are added to this screen by selecting the Sample Manager icon in the left hand corner of the screen and loading saved files as described below Highlight the required files by pressing on the appropriate row and load these into Trace Manager by pressing the Sample Manager icon If the files you require are not displayed on the screen you can scroll through the pages using the up and down arrows Pressing on the Sample ID and Date column headers will sort the files alphabetically and chronologically respectively Note If a USB memory stick is inserted it is possible to toggle between files stored on the internal and USB memories using the icon in the left hand corner The icon in the top right corner will display the memory that is currently in use Trace Manager S
74. rform any calculations This is used for equations that require wavelength measurements of different samples e g chlorophyll analysis You can advance to the next screen at any time by pressing the forward arrow and return to the previous screen by pressing the back arrow Using the Sample Measurement table the user inputs all of the measurements that are required in the method i e the screen left shows a fixed wavelength measurement at 430 0 nm that is named 430 Data is inputted as described below Before any data is inputted Name will read Not set and will not appear in the Sample Data list on the Equation Builder Name Pressing this allows the user to input an alphanumeric name for the measurement The name inputted here will be used as the Sample Data in the Equation Builder inputted data only appears in the Equation Builder if the user has defined a name Wavelength Pressing this produces the number entry box that allows the user to input the A wavelength for measurement Version 2 0 36 Function Pressing this displays a combination box with the following options Abs T at measurement will be at the wavelength inputted by the user only Peak closest to A the instrument automatically finds the peak closest to the inputted wavelength Valley closest to the instrument automatically finds the valley closest to the inputted wavelength Used with Peak closest to A and Valley closest to A onl
75. rinter Internal TAKING A MEASUREMENT E a To perform a measurement insert a cuvette or load directly onto the Lite sample port containing the TT Ponce Mte sap pel E reference solution in the cuvette holder and press the reference button Remove and replace with a cuvette 28b 6 containing the sample or load sample directly onto the CL Wb A ug mt uLite sample port and press the take measurement button A single reference suffices for subsequent analyses in the same series Version 2 0 62 If Background is set to On the A320 result will be included in the left hand column and automatically subtracted from the displayed A260 A280 and A260 A280 results SAVING amp PRINTING For details of manual saving and printing see the Saving and Printing section SAVING amp PRINTING The BioDrop spectrophotometers allow users to save and print sample data This can either be included automatically as a method parameter or performed manually from the sample measurement screen SAVING SAMPLE DATA The BioDrop spectrophotometers allow users to save sample data in three different formats INTERNAL The sample data is saved to the instrument s internal memory format See the Sample Manager section for details on saving and recalling data from the internal memory Note To ensure the optimum performance of the BioDrop TOUCH it is recommended that unwanted data be deleted from the instrument s internal memory at regular intervals
76. rranty withdrawn Troubleshooting Negative absorbance Sample measurements will be negative absorbance reading if the readings absorbance value of the reference is higher than the sample Negative readings can also result if reference and sample are interchanged or if the sample is very dilute and close to the absorbance of the reference Contact your supplier for advice on the minimum concentrations that can be measured Version 2 0 8 Unexpected results Absorbance higher than expected Absorbance lower than expected Poor reproducibility Instrument start up reported failure Version 2 0 Bubbles or contamination in the sample or reference can result in considerable errors If using BioDrop cuvettes check using the bubble viewer provided Incorrect cuvette orientation Rotate by 90 and repeat Incorrect cuvette material for UV measurement wavelengths Wrong pathlength selected in software For Duo models sample placed in cell holder and on micro volume sample platform at the same time Incorrect sample reference Incorrect cuvette orientation Incorrect cuvette material for measurement wavelengths Wrong pathlength selected in software For Duo models sample placed in cell holder and on micro volume sample platform at the same time Contamination in sample or on cuvette For DNA applications check 320nm background if higher than O select background correction in method set up Possible incorrect
77. sed to a path stable but different length of 10mm if a micro volume device like BioDrop CUVETTE is than expected used Note that with a 0 5mm path length the ideal measurement range becomes equivalent when normalised to 2A to 50A and for a path length of 0 125mm it becomes 8A to 200A For unresolved Absorbance issues contact technical support Contacts and Technical Support If you have any problems using your instrument in the first instance please refer to the trouble shooting guide If you require further assistance please get in touch Web http www biodrop co uk Telephone 44 0 203 301 2504 General enquiries enquiries biodrop co uk Support support biodrop co uk Service Repair or Return Good laboratory practice requires that the unit be periodically serviced to ensure optimal performance and can be arranged through your local BioDrop distributor Prior to inspection servicing repair or return the unit must be decontaminated A returns policy operates on this equipment Before returning the equipment to the distributor or manufacturer e Complete a returns request form Available from the BioDrop web site or your local distributor e Return the unit together with a completed declaration of decontamination form available from the BioDrop web site or your local distributor e Please note that the instrument will not be accepted for servicing or return until a completed declaration of decontamination has been recei
78. sorbance of the dye will be measured Note for dyes included in the BioDrop software these values are not editable and this box will be greyed out Numeric entry to 3 decimal places This is the maximum value of the Y axis shown during a kinetics measurement Note the graph will automatically rescale at the end of the measurement to give the optimum Y max 90 Version 2 0 Numeric entry to 3 decimal places This is the minimum value of the Y axis shown during a kinetics measurement Note the graph will automatically rescale at the end of the measurement to give the optimum Y min 91
79. sses and push down firmly Invert the instrument and replace the accessory cover s screws at A and B and add the printer mounting screws at positions C amp D Version 2 0 76 Data Output Pinte Set the built in printer by pressing Settings and Data Output icons Built in Printer Refilling the Printer Paper Lift off the paper cover Place paper roll into printer with paper feeding from bottom Feed printer into slot and turn knob to feed paper Version 2 0 77 Version 2 0 Replace paper cover 78 TECHNICAL SPECIFICATIONS BioDrop TOUCH BioDrop TOUCH PC BioDrop Lite BioDrop Duo 5 7 colour display with Display 7 Capacitive touch panel Pulsed Xenon lamp with 3 year warranty 0 596T at 220nm and 340nm Using NaNO 0 3A to 2 5A 0 to 199 T Photometric Accuracy 0 005A or 1 of the reading whichever is greater at 546nm 5 7 colour display with capacitive touch panel 5nm Photometric 0 003A 0 to 0 5A 0 007A 0 5 to 1 0A Reproducibility 0 005A peak to peak 0 002A RMS 90 250V 50 60 Hz Max 50VA DNA RNA Oligo Dye Labelling Tm DNA RNA Oligo Dye Labelling calculation direct DNA RNA Oligo Dye Labelling Tm Resolution Life l T4 calculation direct UV and UV and colorimetric calculation direct UV and colorimetric Science Software l colorimetric protein methods protein methods protein methods
80. t be controlled by a PC running BioDrop Resolution software The BioDrop TOUCH PC must be connected via USB to a PC and connected to a power supply and the instrument will power up automatically Insert the USB and power cables in the sockets at the back of the instrument Version 2 0 BioDrop TOUCH Controls and Indicators LED on when USB in use On Off switch QUiocDrop 2 Note The off switch is only active from the home screen pressing it whilst any sub menus are displayed takes you back to the home screen pressing again will switch the instrument off BioDrop uLite The BioDrop uLite has an aluminium coated sample port for microvolume analysis BioDrop uLite sample port Version 2 0 BioDrop Duo The BioDrop Duo harbours a sample port and a BioDrop CUVETTE holder for analysis Note Simultanoeus analysis using the microvolume sample port and the BioDrop CUVETTE cannot be carried out INTENDED USERS The instrument is intended to be used by scientists and technicians who possess basic laboratory and technical skills and have the knowledge and understanding of the hazards involved with the unit and the samples used to operate it in a safe manner Instrument Preparation e Switch on the unit and allow it to finish its start up calibration e If applicable connect the unit to a PC using a USB cable and refer to the online help and user manual e Select the appropriate application or meth
81. t directory Note Although it is possible to save an unlimited number of method files to a USB memory stick only 9 can be displayed on the instrument at any one time As these will only be read from the BioDrop Methods folder additional files can be stored in other locations PRINTING PRINTING SAMPLE DATA The BioDrop spectrophotometers allowsusers to print sample data in one of two ways Note Only available printers will be shown in the Print to options box INTERNAL PRINTER Data can be printed to the built in printer when fitted Data is printed with method header instrument serial number time date and all sample results If numerical data is being shown on the display only this data will be printed if graphics are displayed on the screen these will be printed as well as numerical data The built in printer is available as an accessory and can easily be fitted to existing instruments see instructions at the end of this manual PRINT VIA COMPUTER PVC Print via Computer PVC is an application running under Microsoft Windows to enable the BioDrop spectrophotometers to transfer data into a PC environment From there the data can be printed or saved in a variety of formats including graphics and text formats or as an Excel file PVC can store data either to a common directory or be configured to save to independent directories by both file format and instrument serial number PVC is capable of supporting several ins
82. t is essential that the attached PC itself conforms to basic safety and EMC standards and is set up in accordance with the manufacturers instructions If in doubt consult the information that came with your PC The following safety precautions should be observed when operating a PC e To reduce the chance of eye strain set up the PC display with the correct viewing position free from glare and with appropriate brightness and contrast settings To reduce the chance of cross contamination from biological samples use appropriate personnel protection measures and disinfectant wipes on keyboard and mouse Emergency Procedure In the event of contamination malfunction or hazard occurring the operator should disconnect the unit by removing the power cord and isolate for decontamination and or repair Unpacking and Installation e Units weigh less than 4kg No special handling is required e Please keep the original packaging for transport for service or repair as it has been specifically designed to protect the unit from damage during transit e Inspect the instrument and its power supply for any signs of damage caused during transit If any damage is discovered do not use the instrument and report the problem to your supplier e Ensure your proposed installation site conforms to the environmental conditions for safe operation o Indoor use o 5to40 C o Maximum relative humidity 90 up to 31 C decreasing linearly to 50 at 40 C
83. table Separate tables are used for DNA and RNA Calculated factor this is the calculated molecular weight divided by the theoretical absorbance Version 2 0 51 MEASUREMENT PARAMETERS LU Set the required Base Type DNA RNA whether the base is Phosphorylated the Primer Concentration pmoles ml Counterion j i lt m umm E A 7 Buffer Molarity and Counter lon Counter lon has options for Primer Conc Na sodium K potassium TEA triethylammonium and Other allowing the user to set the required molecular weight MW of the counter ion 4 Tm Calculation Set the Pathlength and Integration Time you require Base Sequence allows the user to enter the known base sequence TAA TAC GAC TCA CTA TAG GG triplets using the buttons A C G and T U To improve readability a comma is added after each triplet XIII The Sample Seed entered under Sample will the filename of any automatically saved file Tm Calculation t JL eof pa Tf EE 7 Set the outputs required in your method For more information see the section Saving and Printing Version 2 0 52 TAKING A MEASUREMENT Tm Calculation To perform a measurement insert a cuvette or load directly onto the uLite sample port containing the reference solution in the cuvette holder and press the 250 30 81 Q7 reference button Remove and replace with a cuvette EMEND e containing the sample or load sample directly onto t
84. that will be displayed for each result using alphanumeric entry 40 Using the example above A result of 2100 will return the answer Position 1 a result of 100 and 250 will return the answer Position 2 a result of 50 and 210 will return the answer Position 3 and a result of 10 will return the answer Position 4 Note When using AND or OR logic in an equation the result will be returned as a binary 1 true and 0 false These can be incorporated into the thresholds by setting the Thresholds to 1 Value to 1 and setting the appropriate names as the name above value corresponds to 21 this is the response that will be displayed for true results After all of the thresholds have been set pressing the forward arrow will return the user to the Equation Builder screen The Equation Viewer screen can be accessed using the back arrow Continue as described above until all equations have been created Once complete pressing the forward arrow will take the user to the output options screen below Set the outputs required in your method For more information see the section Saving and Printing Note Automatically saving sample data with sample naming set to Prompt for ID or Fixed list will save the data using the first inputted sample name as the filename Version 2 0 41 PERFORMING A MEASUREMENT NO STANDARDS To perform a measurement insert a cuvette or load directly onto the uLite sample port containing
85. the back arrow This measurement parameters screen allows the user to set the following parameters o Feature Detection Determines the number of peaks or valleys that will be automatically detected Options are Coarse Sensitive or Custom Feature Type The feature types that will be detected by the 4 software Options are Peaks or Valleys Feature Sort Determines the how the features will be displayed in the data table Wavelength shows the peaks in ascending wavelength whilst Magnitude displays then in descending size Draw Peaks When set to ON the width of the peak and the height of the detected peaks will be indicated using dashed lines Version 2 0 25 Custom Peak Height Only displayed if Feature Detection is set to Custom This is the minimum height the peak has to be above the higher of the two adjacent minima for the peak to be detected Custom Peak Width Only displayed if Feature Detection is set to Custom This is the minimum width of the peak as determined by the difference in wavelength between the higher of the two adjacent minima and the opposing intersection of that higher minimum level and the peak profile Single wavelength amp on Set the outputs required in your method For more information see the section Saving and Printing TAKING A MEASUREMENT To perform a measurement insert a cuvette containing the ula c cel QU DERE UE SNO reference solution in the cuvette holder for uLite and Duo
86. tor Source Trace Output Display Selected 1 tart Sage pss S 4 so Tee tstDeivatve J xX 3 tanks andDeivaive J X 4 tanks aperas J xX S Tas smoothed J x Tame Enhanced 4 X z tank Sage pss J x 9 Taws sae pss J X POST SCAN MANIPULATION All recalled files will be displayed on the Trace Manager screen up to 8 The colour of the Slot number will be the colour of the trace when it is displayed on screen To toggle which files are displayed on the measurement screen press in the appropriate Display box up to 8 files can be displayed To select which files data will be displayed on the measurement screen press in the appropriate selected box only one file may be selected Press the forward arrow to view the overlaid data Trace Manager allows the user to manipulate recalled wavescan and kinetics data using the procedure outlined below Trace Manager race auus Ts Selected smwenxs J 4 1st Derivative 2nd Derivative 4th Derivative Smoothed Enhanced Version 2 0 With the required files loaded into Trace Manager press the appropriate Trace Output box to display the manipulation options 31 Wavescan post scan manipulations are Sample Data Displays the raw wavescan data this is the default option 1 4 Derivative Displays the derivative data to the desired order Smoothed Uses the Savitzky Golay algorithm to
87. truments simultaneously limited only by hardware and the speed of the host system and operates via USB cable Installation and operating instructions for PVC can be found on the CD ROM for the respective BioDrop spectrophotometer Version 2 0 73 AUTOMATIC PRINTING k 9t The option to print sample data automatically is set under method parameters With Auto Print set to on the print U location can be set to one of the available options MANUAL PRINTING Sareen If a method does not require sample data to be printed a each time a measurement is taken it is possible to manually EE print sample data This procedure is described below s Set the desired print location in Print to After collecting all Oml required sample measurements select the Print icon from the options menu on the sample measurement screen E Ca Version 2 0 74 Built in Printer Installation Guide This section outlines the method of how to install a built in printer on a BioDrop TOUCH Turn the instrument over and place on a soft surface and screws from positions A and B Turn the instrument back over and lift the accessory cover vertically upwards to remove Remove the tie wrap from the printer cable k Plug the accessory cable into the printer noting the alignment lug Version 2 0 Place the accessory cover on top of the printer and then lower the printer onto the locating bo
88. ur touch screen The BioDrop TOUCH spectrophotometer offers a comprehensive range of spectrophotometric and life science applications The BioDrop uLite is a split beam spectrophotometer which has similar specifications to that of the TOUCH but differs by harbouring a microvolume sample port for analysis The in built sample port has a path length of 0 5mm unlike that of the TOUCH 10mm The BioDrop Duo spectrophotometer displays specifications attributed to both the TOUCH and uLite It contains a sample port for rapid microvolume analysis and offers BioDrop CUVETTE analysis as in the TOUCH A spectrophotometer is an optical device that is designed to transmit a beam of light through a sample Transparent solutions absorb specific wavelengths of light based on their unique molecular composition Absorbance is proportional to concentration of a sample Absorbance peaks of a sample can also be used to identify its molecular composition In kinetic studies the tracking of absorbance over time can be useful to study chemical reactions and biological processes The BioDrop spectrophotometers are designed to emit light from the far ultraviolet 190 nm to the visible light 1100 nm Many materials and in particular solutions of materials will absorb light within this region This makes BioDrop spectrophotometers useful in a wide range of applications including life sciences clinical pharmaceutical cosmetics food amp drink agricultural industrial
89. ved e Instruments that have not been cleaned sufficiently or decontaminated may be subject to additional charges and or return delay Version 2 0 10 Disposal Decontamination In use this product may have been in contact with bio hazardous materials Before disposal the product should be thoroughly cleaned in disinfectant and rinsed with distilled water All outside surfaces and sample areas must be wiped down with disinfectant wipes suitable for purpose and biohazard to which the instrument was exposed WEEE These instruments are covered by the Waste Electrical and Electronic Equipment WEEE Directive and must not to be disposed of as unsorted municipal waste All products marked with this symbol that are to be scrapped must be collected separately and in accordance with local regulatory practice Please contact an authorised representative of the manufacturer for information concerning the decommissioning of your equipment and if required collection Manufacturing Information Requirement Name and address of manufacturer Biochrom Ltd 22 Cambridge Science Park Milton Road Cambridge CB4 OFJ UK Place and date of declaration of conformity Cambridge UK July 2012 Identity of authorised person to sign declaration Sam Luke Managing Director Biochrom Ltd Version 2 0 11 INTRODUCTION TO THE BIODROP SPECTROPHOTOMETERS The BioDrop TOUCH is a standalone easy to use split beam spectrophotometer with a high resolution colo
90. y This is the range over which the instrument will scan for a peak or valley from the inputted wavelength Del Pressing this deletes the row If the data is used in an equation this will also be deleted Equation Editor Sample Naming Specification Sample Id a mum Default Auto Increment Prompt for ID Fixed List Equation Editor has four options for sample naming conventions These are shown below Default The sample name consists of Sample and an incrementing number Auto Increment The sample name is a combination of sample seed and an incrementing sample number The user will be prompted to enter the sample seed for each new batch of samples Prompt for ID The user is prompted to enter the sample name before running each sample Fixed List The user will be prompted to enter the number of samples required Sample names for each sample are then entered on the subsequent screens The inputted sample names are saved for each method Equation E ditor Standard Specification ananas Sel memi Mam T Mam T Mam id Mam T Mam T Mam Version 2 0 The Standard Specification screen is used to declare a list of all of the standard solutions which will be referenced when creating an equation E g the equation for percentage strength at 500 nm compares the absorbance of a sample to the absorbance of a control standard This is where the control standard would be defined 37 Standard na

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BioDrop TOUCH / TOUCH PC/ µLite/ Duo