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Documentation Conventions ............................................................................................... iv

Part I: The DNA Engine

1. Introduction ................................................................................................................. 1-1
2. Layout and Specifications .......................................................................................... 2-1
3. Installation .................................................................................................................... 3-1
4. Operation ...................................................................................................................... 4-1
5. Running Protocols ....................................................................................................... 5-1
6. Creating Programs ...................................................................................................... 6-1
7. Editing Programs ........................................................................................................ 7-1
8. Using the Utilities ........................................................................................................ 8-1
9. Networking .................................................................................................................. 9-1
10. Maintenance ................................................................................................................. 10-1
11. Troubleshooting ........................................................................................................... 11-1

Part II: The DNA Engine Tetrad

12. Information Specific to the DNA Engine Tetrad ..................................................... 12-1

Part III: Accessories

13. The Remote Alpha Dock System .............................................................................. 13-1

Appendix A: Safety Warnings and Guidelines ............................................................. A-1
Appendix B: How a Peltier Heat Pump Works ............................................................. B-1
Appendix C: How a Switching Power Supply Works ................................................. C-1
Appendix D: Shipping Instructions for US Residents .................................................. D-1
Appendix E: Warranties .................................................................................................... E-1
Appendix F: Factory-Installed Protocols ........................................................................ F-1

Index ..................................................................................................................................... In-1

Contents

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Summary of Contents for PTC-0200

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Page 2: ...PTC 0200 DNA Engine PTC 0225 DNA Engine Tetrad Operations Manual Version 4 0 Version 4 0 Version 4 0 Version 4 0 Version 4 0 MJ Research Inc Waltham Massachusetts ...

Page 3: ...es for some types of applications Roche and its licensees provide end user licenses within their respective fields These licenses have dif ferent terms depending on the particular application of PCR and different rules may apply in different countries Anyone who intends to use MJ Research equipment to do PCR is encouraged to contact Hoffmann La Roche for more information at one of the addresses be...

Page 4: ...enance 10 1 11 Troubleshooting 11 1 Part II The DNA Engine Tetrad 12 Information Specific to the DNA Engine Tetrad 12 1 Part III Accessories 13 The Remote Alpha Dock System 13 1 Appendix A Safety Warnings and Guidelines A 1 Appendix B How a Peltier Heat Pump Works B 1 Appendix C How a Switching Power Supply Works C 1 Appendix D Shipping Instructions for US Residents D 1 Appendix E Warranties E 1 A...

Page 5: ...mple Example Select Edit from the Main Menu Graphic Conventions The programming screens displayed in the LCD window are represented by a box containing four lines of text Example Example Example Example Example Terminology Aprogramming option is termed selected when the cursor is positioned in front of it Use the Select keys see fig 2 2 to move the cursor In some screens selected items are also di...

Page 6: ...Part I The DNA Engine ...

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Page 8: ...1 1 1 1 1 1 1 1 1 1 Introduction Meet the DNA Engine 1 2 Using This Manual 1 2 Important Safety Information 1 3 1 ...

Page 9: ...trument types Space saving design for easy setup and transportation Instant Incubate feature for continuous temperature incubations Networking for up to 15 machines for convenient remote operation and documentation of runs Customizable factory installed protocols When multiple users or high throughput operations must be accommo dated the PTC 225 DNA Engine Tetrad is available Essentially consist i...

Page 10: ... Engine or DNA Engine Tetrad begins with a complete understanding of how the machine works Please read this en tire manual before attempting to operate the DNA Engine or DNA En gine Tetrad Do not allow anyone who has not read this manual to oper ate the machine The DNA Engine and DNA Engine Tetrad can generate enough heat to inflict serious burns and can deliver strong electrical shocks if not use...

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Page 12: ... Specifications Front View 2 2 Control Panel 2 2 Back View 2 3 Bottom View 2 3 Alpha Units 2 4 Single Block Models 2 4 Dual Block Models 2 4 Slide Block 2 4 Power Bonnet Accessory 2 4 Specifications 2 5 Gradient Specifications 2 6 2 ...

Page 13: ...ENTION Les blocs peuvent erte tres chauds Pause Stop Cancel Proceed Select Alpha unit lid closed Air intake vents Control panel Thumbwheel DNA Engine Select 3 1 2 4 5 6 7 8 9 0 Proceed Cancel Stop Pause Power Block Instant Incubate A B Block Status Heating Cooling CAUTION Sample blocks may be very hot ATTENTION Les blocs peuvent etre tres chauds MJ RESEARCH PTC 200 Peltier Thermal Cycler Block sta...

Page 14: ...Specifications Back View Figure 2 3 Bottom View Figure 2 4 Air intake vents Power cord jack Alpha unit handle Alpha unit Air exhaust vents also on other side IEEE 488 port Parallel printer port RS 232 port Back Front Air intake vents ...

Page 15: ...oplate 384 Alpha Holds one 384 well microplate or one 96 well microplate Dual Block Models 30 30 Dual Alpha Holds 2 x 30 x 0 5ml tubes 30 48 Dual Alpha Holds 1 x 30 x 0 5ml tubes and 1 x 48 x 0 2ml tubes 48 48 Dual Alpha Holds 2 x 48 x 0 2ml tubes or half plates Slide Block Twin Tower Holds 2 x 16 standard slides Power Bonnet Accessory Permits remote control of Alpha unit lid opening avail able fo...

Page 16: ...capacity Varies with installed Alpha unit Line voltage 100 240VAC rms no adjustment needed among volt ages within these ranges Frequency 50 60Hz single phase Power 850W maximum Fuses Two 6 3A 250V 5 x 20mm Displays One 20 x 4 LCD alphanumeric display Ports One 25 pin 8 bit parallel interface printer port One 9 pin RS 232 serial port for printer or remote use One IEEE 488 bidirectional general purp...

Page 17: ... timer starts for the gradient step NIST traceable Column uniformity 0 4 C well to well within column within 30 sec onds of reaching target temperature Calculator accuracy 0 4 C of actual well temperature Lowest programmable 30 C temperature Highest programmable 105 C temperature Temperature differential 1 24 C range ...

Page 18: ...klist 3 2 Setting Up the DNA Engine 3 2 Environmental Requirements 3 2 Power Supply Requirements 3 3 Air Supply Requirements 3 3 Ensuring an Adequate Air Supply 3 3 Ensuring That Air Is Cool Enough 3 4 Requirements for Robotics Installations 3 5 3 ...

Page 19: ...in case you need to return the DNA Engine for service See appendix E for shipping instructions Setting Up the DNA Engine The DNAEngine requires only minimal assembly plugging in the power cord and inserting an Alpha unit Insert the power cord plug into its jack at the back of the machine see fig 2 3 for location of jack then plug the cord into an electrical outlet With the machine turned off inser...

Page 20: ...rtain it is inscribed with the trademark of UL CSA TUV VDE or another national testing agency N N N N Note ote ote ote ote Do not cut the supplied 120V power cord and attach a different con nector Use a one piece molded connector of the type specified above Air Supply Requirements The DNA Engine requires a constant supply of air that is 31 C or cooler in order to remove heat from the Alpha unit s ...

Page 21: ...30 minutes to warm up the DNA Engine then measure the air temperature at the back air intake vents If more than one machine is involved measure the air temperature for each If the air intake temperature of any machine is warmer than 31 C use table 3 1 to troubleshoot the problem Some experimentation may be required to determine the best solution when more than one cause is involved After taking st...

Page 22: ...with other heat generating equip ment Overheating can quickly occur when many of these machines are operating at once unless preventive measures are taken Follow the procedures described above to ensure adequate airflow and an air intake temperature of 31 C or cooler Air intake temperature must be verified by measurement Do not use oil to thermally couple sample vessels to the blocks of ma chines ...

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Page 24: ...es 4 6 Sealing Sample Vessels 4 7 Sealing with Oil or Wax 4 7 Sealing with the Hot Bonnet and Caps or Film Sheets 4 7 Adjusting the Hot Bonnet s Lid Pressure 4 8 Loading Sample Vessels into the Block 4 9 Using Oil to Thermally Couple Sample Vessels to the Block 4 9 Using the Optional Probe 4 10 Customizing the Probe Vessel 4 10 Adding the Oil 4 11 Loading and Connecting the Probe 4 11 Detecting a ...

Page 25: ... sink is not at ambient tempera ture typically because the Alpha unit was recently in use the machine will skip the self test If the self test does not detect any problems the Main Menu is displayed The DNA Engine is now ready to execute programs Understanding the Main Menu The Main Menu is the common access point to all programming and machine configuration screens Run Executes a program Enter Al...

Page 26: ...entry Stop Terminates a running protocol Pause Pauses a protocol during execution accesses Japanese Katakana syllabary Instant Incubate Initiates a program that sets up the DNA Engine as a simple incubator Block Selects a different block when using a dual block Alpha unit switches between block screens and the Main Menu in the LCD win dow during a protocol run Status Indicator Lights Power light G...

Page 27: ...th Power Bonnets Installing an Alpha Unit 1 Turn the DNA Engine off see the Caution on p 4 5 2 Hold the Alpha unit at its front and back edges 3 Lower the Alpha unit into the DNA Engine base leaving at least 3cm between the front edge of the Alpha unit and the front of the base 4 Raise the handle at the back of the Alpha unit and slide the block forward as far as it will go fig 4 1A 5 Push the han...

Page 28: ...n Alpha Unit Grip the front edge of the top lever of the Hot Bonnet as shown in figure 4 2A and pull upward firmly The top lever will pop open to reveal the entire thumbwheel fig 4 2B Continue pulling upward to open the Hot Bonnet The Hot Bonnet will tip backward revealing the entire block Caution Caution Caution Caution Caution Do not pull on the thumbwheel to open the unit This can damage the Ho...

Page 29: ... the wells snugly Since these tubes were originally designed for centrifuges some brands may not fit tightly in thermal cycler wells Thin walled 0 5 ml tubes were specifically de signed for thermal cycling and the higher quality brands provide a good and consistent fit MJ RESEARCH provides thin and thick walled 0 5 ml tubes designed for precise block fit 0 2 ml Tubes All types of thin walled 0 2 m...

Page 30: ...e concentration of reactants Only a layer of oil or wax will completely prevent evaporation from sample vessels However an adequate degree of protection can be achieved by sealing with Microseal film or caps then cycling the samples using the heated lid to prevent condensation refluxing Sealing with Oil or Wax Mineral oil silicone oil paraffin wax or Chill out liquid wax may be used to seal sample...

Page 31: ...ed to seal tightly during cycling yet release smoothly which minimizes the risk of aerosol formation and cross contamination of samples Microseal A is easily cut for use with fewer than 96 wells Microseal M rubber sealing mats are an economical means to seal 96 well microplates An array of 96 dimples on the mat helps orient it on the microplate and prevents the mat from sticking to the Hot Bonnet ...

Page 32: ...nner lid has touched the microplate tubes 5 Open the Hot Bonnet Turn the thumbwheel clockwise an extra half to three quarters of a turn to set an appropriate lid pressure Caution Caution Caution Caution Caution Do not turn the thumbwheel more than three quarters of a turn This can make it hard or impossible to close the lid and puts excessive strain on the latch holding the lid closed An extra hal...

Page 33: ... do not run accurately when oil is used Oil traps dirt which interferes with thermal contact between vessels and the block Caution Caution Caution Caution Caution If you use oil in the block use only mineral oil Never use silicone oil It can damage the Alpha unit One exception to this recommendation involves the use of volatile radioac tive 35 S nucleotides A small amount of oil in the block can h...

Page 34: ... protocols for probe control Note Note Note Note Note Because the thermal characteristics of a probe can never precisely match those of a sample calculated control is often a better choice than probe control Customizing the Probe Vessel For the most precise control of sample temperatures install the probe s thermistor in the same type of tube that the samples will be placed in This is particularly...

Page 35: ...ons 1 x the volume of the buffer in an individual tube plus 1 x the volume of oil overlay if one is used It is important to use the correct amount of oil so that the representative sample changes temperature at the same rate as the actual samples To add the oil open the sample tube and pipette in the appropriate amount The oil must completely cover the thermistor Light and heavy silicone oil may a...

Page 36: ...ls to the Block p 4 9 Plug the probe into the jack at the back of the block so that the wire is to the left of the plug fig 4 4 Detecting a Faulty Probe If the DNA Engine detects that the probe is broken or missing when a protocol begins running the protocol s temperature control method is automatically switched from probe control to calculated control and the following message is immediately disp...

Page 37: ...m 2 0 0 6 l m 5 0 0 3 l m 5 0 6 1 6 1 e d i l s n o i t p i r c s e D R J M H C R A E S E g o l a t a C l a e s o r c i M m l i f A 1 0 0 5 A S M l a e s o r c i M t a m M l a e s o r c i M d a p P p i r t S 8 s p a c 1 0 8 0 S C T p i r t S 2 1 s p a c 1 0 2 1 S C T l a e S f l e S t n e g a e r 1 0 1 0 R L S l a e S e m a r F s r e b m a h c s e i r e s F L S s e t a l p o r c i m l l e w 6 9 e ...

Page 38: ...sfer The thin walls are somewhat fragile and can craze or develop small cracks when subject to mechanical stress Undamaged thin polypropylene tubes may also be somewhat permeable to the 35 S break down product Either way there have been reports of 35 S passing through the walls of 0 2 ml tubes of several different brands during thermal cycling No data are yet available on radio active contaminatio...

Page 39: ...ford Illinois Pierce Eurochemie B V Holland Micro Cleaning Solution Cole Parmer Niles Illinois and Dow Bathroom Cleaner avail able in supermarkets Caution Caution Caution Caution Caution Harsh cleaning agents are corrosive to aluminum and must never be used on bare aluminum blocks MJ RESEARCH blocks are anodized so they have a protective coating of aluminum oxide Still harsh agents such as those a...

Page 40: ...osity 50cs Volume to use 1 7 x volume of buffer in individual sample tube plus one volume of oil overlay Dow Corning 200 heavy silicone oil dimethypolysiloxane Sigma DMPS V Density 0 97g ml Viscosity 5cs Volume to use 2 7 x volume of buffer in individual sample tube plus one volume of oil overlay Note Note Note Note Note Use these oils only in the proportions outlined above Using them in any other...

Page 41: ...rol Protocol 5 4 Setting Up a Probe Control Protocol 5 5 Reading the Runtime Screen 5 5 Switching Between the Runtime Screen and the Main Menu 5 6 Reading the Protocol Completion Screen 5 6 Printing a Log for a Running Program 5 7 Manually Stepping Through a Protocol 5 8 Pausing a Running Protocol 5 8 Stopping a Running Protocol 5 9 Resuming a Protocol after a Power Outage 5 9 Using the Instant In...

Page 42: ...on whether custom protocols have been stored in the MAIN folder or in custom folders If all protocols have been stored in the MAIN folder The first of three or more screens listing the protocols will be displayed Custom protocols are listed first then the 14 factory installed programs Use the Select keys to scroll through the listed protocols Scroll past the last or first listed protocol to see th...

Page 43: ...n The status indicator light for the selected block will flash green Setting Up the Temperature Control Method When the protocol is selected and the correct block is designated for a dual block Alpha unit one or more screens will be displayed These screens will ask for information needed to set up the block s temperature control method The DNA Engine can control the block s temperature in three di...

Page 44: ...te See Using Calculated Control in the Twin Tower Block Opera tions Manual for information on specifying slide format A screen asking for the sample reaction volume last line in example below Use the keypad to enter a sample volume in microliters then press Proceed If sample vessels are sealed with oil or wax include the volume of the oil or wax in the total sample volume entered Note Note Note No...

Page 45: ...now To avoid this press Cancel install the probe and set the protocol up again When the probe verification screen is displayed press Proceed to be gin the protocol run Reading the Runtime Screen During a protocol run a runtime screen will be displayed The screen lists the protocol name 2 STEP in the example above proto col step that is running 1 cycle number 1 method of temperature control Calc an...

Page 46: ...e run This screen is also displayed only as long as the key is pressed The runtime screen returns when you stop pressing the key Switching Between the Runtime Screen and the Main Menu Press Block to toggle between the runtime display and the Main Menu This allows you to edit a stored program enter a new one print a pro gram run another protocol on a dual blockAlpha unit or networked DNA Engine or ...

Page 47: ... that a printer is connected to the machine See Printing a Program chapter 8 for information about compatible printers Follow the instructions under Choosing a Printer Port chapter 8 to prepare the DNA Engine to communicate with your printer As long as a printer is connected to the machine the following screen will appear whenever a protocol is run To print the protocol as it runs select Yes then ...

Page 48: ...ram The timer in the lower right hand corner of the runtime screen will be replaced by the word Pause The samples are held at the displayed temperature until either the Pause or the Proceed key is pressed which causes the protocol run to re sume A protocol cannot be paused before the target temperature for a given step has been reached If Pause is pressed before this point the block continues heat...

Page 49: ...curs when a protocol is running the DNA Engine will hold the protocol in memory for a minimum of 24 hours to a maxi mum of 7 days depending on environmental conditions When power is restored the protocol will begin running again at the point at which it was stopped and a notice about the power interruption will be displayed The notice will identify the step and the cycle that were running when the...

Page 50: ...temperature from 5 0 C to 105 0 C then press Proceed The DNAEngine will incubate the sample at the specified temperature until Cancel or Stop is pressed When the sample block reaches the incubation temperature a timer be gins running in the lower right hand corner of the screen To stop and start the timer press Pause Tip Tip Tip Tip Tip The Pause feature is useful if you need to temporarily remove...

Page 51: ...erature Control Method 6 6 Entering the Program s Steps 6 6 Entering a Temperature Step 6 7 Entering a Gradient Step 6 9 Editing a Gradient Step 6 10 Reviewing a Gradient Program 6 10 Using the Gradient Calculator 6 10 Factory Installed Gradient Program 6 12 Entering a Ramp Step 6 12 Entering a GoTo Step 6 14 Entering the End Step 6 15 Modifying a Program Step with the Options 6 16 Entering an Inc...

Page 52: ...from left to right The maximum programmable temperature is 105 C the minimum programmable temperature is 30 C 3 Ramp step optional Sets a slower than maximum rate of heating or cooling 4 GoTo step optional Causes the program to cycle back to an earlier step for a specified number of times up to 9 999 times 5 End step mandatory Instructs the DNA Engine to shut down its heat pump because the program...

Page 53: ...t follow back to the GoTo step When the program has returned or cycled back to the step a specified number of times the program moves on to the step that follows the GoTo step For example consider a basic cycle sequencing protocol consisting of 30 repeats of a denaturation and an annealing extension step Rather than listing all 60 steps use a GoTo step to design a short easy to enter pro gram Raw ...

Page 54: ...es are controlled much more accurately than with block or probe control Hold times can be shortened significantly when protocols are run under calculated control In addition to the simple convenience of spending less time running reactions shorter protocols also help preserve enzyme activ ity and minimize false priming Cycling denaturations run under calculated control are usually optimal at 5 sec...

Page 55: ...m each temperature step Some empirical testing may be required to adjust modified programs for opti mum performance Modifying a Program Designed for a Different Machine The ramp programming step can be used to adapt programs designed for thermal cyclers with slower maximum heating and cooling rates than the DNA Engine In addition a given protocol will occasionally work better with a slower rate of...

Page 56: ...n the character needed is displayed next to Name press Proceed The character will be accepted and the cursor will move one space to the right Numbers and dashes may also be inserted by pressing the corre sponding keys on the keypad When the name is complete press Proceed once to accept the last char acter and again to accept the whole name If the name is already in use for a program a screen sayin...

Page 57: ...cond line of this screen shows the number of the step being programmed 1 is used in the example above The last line of the screen allows a target temperature in degrees Celsius to be entered for the step Use the keyboard to enter any number between 5 0 and 105 0 as the target temperature 92 0 is used in the example below Press Proceed The target temperature will move to the second line of the scre...

Page 58: ...time for the step Option displays the Options Menu see Modifying a Program Step with the Options p 6 11 Tip Tip Tip Tip Tip Avoid programming many short holds of only a few seconds each This can overheat the block causing the HS Overheat ing or PS Overheating error messages to be displayed and triggering automaticAlpha unit shutdowns if the block exceeds its maximum allowable temperature Entering ...

Page 59: ... a hold time for the temperature gradient step Enter CUSTOM1 2 50 0 to 70 0 Time Enter the hold time in the form of min sec Press Proceed Aconfirma tion screen will appear Enter CUSTOM1 2 50 0 to 70 0 for 0 30 OK Yes No Option Select Yes to enter the step into memory and proceed to the next step select No to reject or edit the current step To preview select Option then Preview Preview gives the pr...

Page 60: ... Column 12 70 0 right Scroll up and down the screen using the Select keys When scrolling the Gradient Review line will be held constant while the lower 3 lines can be manipulated up or down The temperatures displayed will be for each of the twelve wells along the long axis of the sample block These temperatures will be predicted from an algorithm as a steady state tem perature of the block and the...

Page 61: ...ent using the number keys and Proceed key You may enter inte gers without decimal points The following screen will be displayed Gradient Calculator Column 1 50 0 left Column 2 50 5 Column 3 51 5 Column 4 53 2 Column 5 55 5 Column 6 58 4 Column 7 61 8 Column 8 64 6 Column 9 66 8 Column 10 68 4 Column 11 69 6 Column 12 70 0 right You may scroll up and down the screen using the Select keys When scrol...

Page 62: ...he example below Note Note Note Note Note If a ramp rate faster than the Alpha unit s maximum rate of heat ing and cooling is entered the maximum rate will be used Press Proceed The ramp rate will move to the second line of the screen and a line allowing entry of a finish temperature for the ramp step will be displayed Enter the finish temperature for the ramp step 69 C is used in the ex ample bel...

Page 63: ...ecuted To hold the block for some period of time at a ramp step s fin ish temperature make sure a temperature step immediately follows the ramp step and program the hold at the finish temperature into this step Entering a GoTo Step To enter a GoTo step select GoTo from the Enter Menu The first GoTo screen will be displayed The second line of this screen shows the number of the step being pro gramm...

Page 64: ...t line Select one of the displayed choices then press Proceed Yes accepts the step and displays the Enter Menu again Use the En ter Menu to enter the next step in the program No allows reentry of the step number and number of additional cycles Entering the End Step To enter the End step select End from the Enter Menu The single End screen will be displayed This screen automatically enters End on o...

Page 65: ... from theconfirmationmenuofatemperatureorrampstep thenpress Proceed The Options Menu will be displayed on the bottom line of the screen Inc modifies a temperature step with an increment option An incre ment option allows a progressive increase or decrease of temperature each time the step is executed in a GoTo cycle Ext modifies a temperature step with an extend option An extend op tion allows a p...

Page 66: ...l move to the third line of the screen and a confirmation menu will be displayed on the last line Select one of the displayed choices then press Proceed Yes accepts the Inc value and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the Inc value Option displays the Options Menu again Use the Options Menu to enter another option for the ste...

Page 67: ...ne of the displayed choices then press Proceed Yes accepts the Ext value and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the Ext value Option displays the Options Menu again Use the Options Menu to enter another option for the step Entering a Beep Option To enter a beep select Beep from the Options Menu for a temperature step or a ram...

Page 68: ...just made will be cancelled so that another value may be entered or another menu option chosen Press Proceed after changing a value so that the program will accept it To Change All the Values in the Step Being Entered Repeatedly press Cancel Each time you press the key the cursor will move backward through the values for the step deleting the values as it moves When all values for the step have be...

Page 69: ...r adding an option To abandon the Edit Menu and return to the list of program steps press Cancel To enter Edit mode Move the cursor to the number of the step you wish to edit then press Proceed See chapter 7 for information on entering Edit mode If you do not wish to enter Edit mode press Can cel The screen will return to the list of program steps To delete the program Position the cursor on any s...

Page 70: ...ou can begin a new program Keeping a Permanent Record of Programs Occasionally in the course of repairing a defective DNA Engine it is necessary to replace the chip that stores all custom user protocols To avoid losing your protocols in such an event always maintain an up to date record of them Protocols may be printed out using the List utility see chapter 8 stored on a computer using the DNA Eng...

Page 71: ... Editing Programs Editing a Stored Program 7 2 Initiating Editing 7 2 Editing the Program 7 3 Inserting a New Step 7 4 Deleting a Step 7 4 Adding an Option 7 4 Saving an Edited Program 7 4 Cancelling Editing Changes 7 5 7 ...

Page 72: ...en will be displayed depending on whether your programs have been stored in the MAIN folder or in custom folders If all programs have been stored in MAIN The screen will list the contents of MAIN Select the program to be edited then press Proceed If programs have been stored in custom folders The screen will list all the folders residing in the machine Select the folder containing the program then...

Page 73: ...ual value in a step position the cursor on it and type the new value then press Proceed The new value will be dis played on the screen To cancel a change press Cancel The original value will be restored To add or delete a step or to modify a step with an option position the cursor on the step number then press Proceed The Edit Menu will be displayed for that step Edit displays the previous screen ...

Page 74: ... a deletion see Cancelling Editing Changes p 7 5 Note Note Note Note Note Be careful when using Delete Once a step has been deleted it cannot be recovered without abandoning all editing changes that have been made in the program This could be inconvenient if the program has been extensively edited Adding an Option To add an option to a step select Option from the Edit Menu then press Proceed The o...

Page 75: ...allows another step to be added just before the End step Cancelling Editing Changes To cancel all editing changes made to a program use the Select keys to move the cursor to any step number then press Cancel A cancellation confirmation screen will be displayed Select Yes then press Proceed All editing changes will be abandoned and the Main Menu will be displayed Edit CUSTOM1 Cancel changes _YES No...

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Page 77: ... Renaming a Program 8 5 Moving a Program 8 5 Deleting a Program 8 5 List Utilities 8 6 Viewing a Program in the LCD Window 8 6 Printing a Program 8 7 Setup Utilities 8 7 Choosing a Remote Port 8 7 Choosing a Printer Port 8 8 Choosing a Minimum Block Temperature for the Hot Bonnet 8 9 Choosing a Temperature Control Method for the Hot Bonnet 8 9 Determining the Software Version Number 8 10 8 ...

Page 78: ...een stored in custom folders The screen will list all the folders residing in the machine Select the folder containing the program then press Proceed Alist of all programs in the folder will be displayed Select the desired pro gram then press Proceed File Utilities Use these utilities available from the Files Menu to accomplish the fol lowing tasks Create folders to store programs in Assign passwo...

Page 79: ...der cannot be edited renamed or deleted nor can new protocols be placed in the folder without the pass word Users without knowledge of the password can still run copy and view a program Note Note Note Note Note A password cannot be assigned to the MAIN folder To assign a password to a folder select Secure from the Files Menu then press Proceed A list of all folders in the machine will be displayed...

Page 80: ...folders in the machine will be displayed Select the folder to be deleted then press Proceed Aconfirmation screen will be displayed Select Yes then press Proceed The folder will be deleted and the Main Menu will be displayed To cancel the deletion press Cancel or select No and press Proceed Copying a Program The copy utility copies a program and gives the copy a new name Cop ies can be placed in th...

Page 81: ...er 6 then press Proceed The program will be renamed and stored and the Main Menu will be displayed Moving a Program To move a program select Move from the Files Menu then press Pro ceed Locate the program to be moved see Locating a Stored Pro gram p 8 2 then press Proceed A screen listing all folders will be displayed Select the folder the program should be moved to then press Proceed The program ...

Page 82: ...inter is connected A screen will be displayed asking whether the program should be sent to the printer Select No then press Proceed The program will be listed in the LCD window The first listed screen will show the program s control method Press Proceed to view subsequent screens listing each program step including any options Use the Select keys to scroll up or down through the steps one line at ...

Page 83: ...ngine see Choosing a Printer Port p 8 8 Select List from the Main Menu then press Proceed Locate the program to be printed see Locating a Stored Program p 8 2 then press Pro ceed The screen asking whether the program should be sent to the printer will be displayed see above Select Yes then press Proceed The program will be printed Setup Utilities Use these utilities available from the Setup Menu t...

Page 84: ...e displayed on the last line of the screen The machine s current address will be displayed To change it enter a number from 0 30 then press Proceed The remote port assign ment will change to IEEE 488 the address number will be assigned to the machine and the Main Menu will be displayed Note Note Note Note Note Do not choose 0 for the machine address unless the DNA Engine will be a controller in a ...

Page 85: ...acking Offsets the temperature of the heated inner lid at least a specified number of degrees Celsius in comparison to the tempera ture of the sample block Constant Keeps the inner lid at a specified temperature C The DNA Engine is set for the tracking mode at the factory using an offset of 5 C which should be adequate for most reactions The constant mode is provided for unusual reactions requirin...

Page 86: ...sary to determine the version number of the software installed in the DNA Engine e g to report a problem to MJ RESEARCH To do this select Version from the Setup Menu then press Proceed The current version number will be displayed The top line reports the software version number 1 1L in the example The other two lines refer to the four pages that the software has been broken into and their associat...

Page 87: ...ithout a Computer 9 2 Connecting the Machines 9 2 Assigning Address Numbers to Machines 9 2 Running a Protocol on Networked Machines 9 3 Networking Machines with a Computer 9 4 Creating a Computer Controlled IEEE 488 Network 9 5 Creating a Computer Controlled RS 232 Network 9 5 9 ...

Page 88: ... machine and then be run on all the other machines connected to the network Networking Machines Without a Computer Connecting the Machines Connect DNA Engines and DNA Engine Tetrads via the IEEE 488 port on the back of each machine see figs 2 3 and 12 4 using high quality cables Although several connection configurations are possible we recommend a simple daisy chain or star pattern The DNA Engine...

Page 89: ... the controller Local indicates that this is the controller s network screen and 96V indicates the type of Alpha unit loaded into the controller If a dual block Alpha unit is loaded into the controller press Proceed until the letter designating the desired block is displayed after the aster isk in the upper right hand corner of the screen The letter A designates the right hand block and the letter...

Page 90: ...ontroller s LCD win dow The LCD window of the machine holding the active block will con tinue to show whatever screen it was displaying before the protocol be gan running Press Block to display the Main Menu on the controller again Repeat the procedure to run protocols on other networked blocks Press Block on the controller to progressively display the runtime screens of all net worked blocks that...

Page 91: ... of the networked machines have been assigned IEEE 488 address 0 as this will cause communication problems with the computer Install the MJ RESEARCH DNA Engine Driver software on the computer and use it to control the network Creating a Computer Controlled RS 232 Network In a computer controlled RS 232 serial network each machine in the network is connected directly to the controlling computer via...

Page 92: ......

Page 93: ... 1 10 1 10 1 Maintenance Cleaning the DNA Engine 10 2 Cleaning the Chassis and Block 10 2 Cleaning the Air Vents 10 2 Cleaning Radioactive or Biohazardous Materials Out of the Block 10 3 Changing the Fuses 10 3 10 ...

Page 94: ...ls whenever the oil has become discolored or contains particulate matter Use a swab to determine whether cleaning is needed Clean the block with 95 ethanol as described above Oil buildup must be prevented Old oil harbors dirt which interferes with vessel seating and diminishes thermal coupling of sample vessels to the block Caution Caution Caution Caution Caution Do not pour any cleaning solution ...

Page 95: ... incorporates neutral fusing which means that live power may still be available inside the unit even when a fuse has blown or been removed Never open the DNA Engine base You could receive a serious electrical shock Opening the base will also void your warranty 1 Disconnect the power cord from the back of the instrument Move the power switch to the 0 off position 2 Insert one corner of a small flat...

Page 96: ......

Page 97: ...11 1 11 1 11 1 11 1 11 1 Troubleshooting 11 Error Messages 11 2 Problems Related to Protocols 11 6 Problems Related to Environmental Conditions Setup and Maintenance 11 8 ...

Page 98: ... a e r a w t f o s s e n i h c a m e n i m r e t e D f I 9 8 p e e s r e b m u n n o i s r e v t c a t n o c M 1 1 w o l e b s i r e b m u n R J M H C R A E S E s i d l a c o l r u o y r o e r a w t f o s a t s e u q e r o t r o t u b i r t e d a r g p u n o i s r e v o t e s a b s w o l l a n o i t c n u f l a m r o s n e S l a m u m i x a m s t i r e v o k c o l b t a e h g n i r e g g i r t e r...

Page 99: ... e s r e l o o c r o C 1 3 s m e l b o r p y l p p u s r i a t c e r r o C r o r r e f I n i a g a l o c o t o r p n u r d n a y a m e s a b s t s i s r e p e g a s s e m J M t c a t n o C g n i c i v r e s d e e n R H C R A E S E l a c o l r u o y r o r o t u b i r t s i d l o c o t o r p a g n i n n u r s i e n i h c a M a y l n o f o s e l c y c y n a m f o g n i t s i s n o c t a e h t i n u a...

Page 100: ...e c n a l a b m I r e w o P R L t i n u a h p l A n i s t i n u c i r t c e l e o m r e h T y l m r o f i n u g n i t a e h t o n e r a k c o l b g n i r e v i l e d s n i g e b e n i h c a m o s e l e g n i t a e h l l a o t r e w o p l a u q e n u r e b l l i t s y a m s l o c o t o r P s t n e m n u o t e u d l i a f y a m s n o i t c a e r t u b s e r u t a r e p m e t k c o l b n e v e g n i ...

Page 101: ...o l r u o y r o r o t u b i r t s i d g n i l c y C k c o l B w o l S n o o S a h p l A e c i v r e S d e h c a e r t o n s a h k c o l b t i n u a h p l A t c e p x e n i h t i w e r u t a r e p m e t t e g r a t g n i p e e b n i g e b l l i w t i n U e m i t d e l i t n u p e e b o t e u n i t n o c l l i w d n a o r p d e h c a e r s i e r u t a r e p m e t t e g r a t s t i o t d e s s e r g ...

Page 102: ...i l a e n n a d n a n o i t a r t o r p d e r i s e d e z i m i x a m o t e r u t a r e m i r p e z i m i n i m d n a t c u d s r e m i d t u b g n i k r o w n o i t c a e R a r t x e d e t c e p x e n u s i r a e m s r o s t c u d o r p n e e s r u c c o n o i t a z i d i r b y h c i f i c e p s n o N p u t e s g n i r u d g n i r e h t o t n i t r a t s t o h a m a r g o r P l o c o t o r p n o ...

Page 103: ... r g l o r t n o c e r u t a r e p m e t g n o r W d e s u d o h t e m k c e h c o t y t i l i t u t s i L e s U r o f d o h t e m l o r t n o c e r u t a r e p m e t d e d e e n f i e g n a h c l o c o t o r p o t e n i h c a m g n i s u a c d e l i a f e b o r P d e t a l u c l a c r e d n u l o c o t o r p n u r l o r t n o c e r u l i a f e b o r p r o f n e e r c s k c e h C d e e n y a m e b...

Page 104: ...f o s n o i t y v a e h t u o m u u c a V h t o l c p m a d s r e p a p y n a e v o m e R s n o i t c e l l o c i s o P e n i h c a m e h t r e d n u d e c a l p m o r f m c 0 1 t s a e l t a e n i h c a m n o i t s e c a f r u s l a c i t r e v s i s t n e v e k a t n i o t n i g n i w o l f r i A t o n C 1 3 r e t n e r i a f o e r u t a r e p m e t k c e h C g n i w o l l o f s t n e v e k a t ...

Page 105: ...Part II The DNA Engine Tetrad ...

Page 106: ......

Page 107: ...ements 12 6 Operating the DNA Engine Tetrad 12 7 Turning the DNA Engine Tetrad On 12 7 Operating Alpha Units 12 7 Running Protocols on the DNA Engine Tetrad 12 7 Running Separate Protocols by Block 12 7 Running the Same Protocol on All Blocks 12 8 Running an Instant Incubation 12 8 Cancelling Protocols 12 8 Programming the DNA Engine Tetrad 12 9 Networking the DNA Engine Tetrad 12 9 Software Requi...

Page 108: ...DNA Engine Tetrad is viewed from above fig 12 1 The DNA Engine Tetrad s power supply has been placed in a separate housing that is attached by cables to the base which keeps the base com pact and makes it easier to use in robotics installations The power sup ply uses MOSFET transistors to efficiently convert AC input power into the high current low voltage DC power that the Tetrad requires see ap ...

Page 109: ...Block 1 4 7 2 5 8 3 6 9 0 Pause Stop Power supply Dual block Alpha unit Single block Alpha unit Front air exhaust vents Control panel Power supply air intake vent Tetrad base 2 1 3 4 5 6 7 8 9 0 Stop _ Pause MJ RESEARCH PTC 225 Peltier Thermal Cycler Power CAUTION Sample blocks may be very hot ATTENTION Les blocs peuvent etre tres chauds Block Status DNA Engine Tetrad Cancel Proceed Select Block I...

Page 110: ...ual Back View Figure 12 4 Alpha units removed Bottom View Figure 12 5 Tetrad base Cables plug in here Signal cable Power cable Power supply Power supply air exhaust vents Electrical outlet plug RS 232 port IEEE 488 port Parallel printer port Back Front Air intake vents ...

Page 111: ...se save the original packing materials in case you need to return the Tetrad for service See appendix E for shipping instructions Installation The DNAEngine Tetrad requires minimal assembly installing the Alpha units see chapter 4 and connecting the signal and power cables to the back panel of the base Connecting the Cables The signal and power cables running from the DNA Engine Tetrad s power sup...

Page 112: ...the specified range without adjustment so there is no voltage setting switch Environmental Requirements The requirements for safe operation of the DNA Engine Tetrad are the same as those of the DNA Engine see chapter 3 Air Supply Requirements The air supply requirements for the DNA Engine Tetrad are the same as those of the DNA Engine see chapter 3 Robotics Installation Requirements Robotics insta...

Page 113: ...cols on the DNA Engine Tetrad Running Separate Protocols by Block Choose a protocol see chapter 5 A screen identifying the protocol 2 STEP in the examples below the Alpha unit type 96V and the quad rant number of the block the protocol will run on 1 will be displayed If a dual block Alpha unit is present in the identified quadrant an A or a B will appear after the quadrant number e g 1A Protocols ...

Page 114: ...s at once To do this select a protocol or press Instant to run an instant incuba tion then press Block until All appears in the upper right hand corner of the displayed screen The status indicator lights for all of the sample blocks will be flashing green Press Proceed to run the protocol on all the blocks simultaneously Running an Instant Incubation Instant incubations are run in the same way as ...

Page 115: ...have software version 1 1J or later in order to control a network that includes one or more DNA Engine Tetrads To identify the software version loaded into a DNAEngine see Determining the Software Version Number chapter 8 Operating Networked DNA Engine Tetrads Networked DNA Engine Tetrads operate the same as networked DNA Engines Each block of a networked DNAEngine Tetrad is designated by the mach...

Page 116: ... acting fuse 0 25 x 1 25 3AB or 3ABC To replace a fuse first unplug the power supply from the wall Twist the fuse cap a quarter turn to the left and pull out the fuse plug Replace the blown fuse Press the plug back into its socket and twist it a quarter turn to the right to seat it The plug is spring loaded so firm pressure may be required Warning Warning Warning Warning Warning The DNA Engine inc...

Page 117: ...Part III Accessories ...

Page 118: ......

Page 119: ...13 1 13 1 13 1 13 1 13 1 The Remote Alpha Dock System About the Remote Alpha Dock System 13 2 Packing Checklist 13 3 Requirements 13 3 Installation 13 5 Operation 13 6 13 ...

Page 120: ... space and facilitating robotic operation The basic system the RAD 0200 comprises a Dock Connector which mounts in the base and a Re mote Alpha Dock into which the Alpha units are mounted The RAD 0201 contains in addition a fan power supply and three daisy chain series cables allowing the cooling fans for up to four Remote Docks to run off a single AC outlet Additionally the fan power supply along...

Page 121: ...mote Alpha Dock System allows for custom installations The following placement configurations are recommended by MJ Research Remote Docks with mounted Alpha units may be configured in any horizontal orientation or array as long as a minimum side clearance of 10 cm is maintained between the Remote Dock and any wall bulk head or adjacent Remote Dock unit this is identical to the PTC 200 PTC 225 base...

Page 122: ...obotic operation as long as the airway beneath the unit is equivalent to the airway the unit would have with the feet attached Usually a hole will need to be cut to allow air to flow to the the cooling fan Figure 13 5 is a template for flush mounting the Remote Dock Power Supply The Alpha unit mounted in each Remote Dock is powered from the PTC 200 or PTC 225 base The Remote Dock s fan is powered ...

Page 123: ...K DATA Attach the CONNECTOR DATA end to the female connector labeled DATA on the circuit board and slide the latch to lock the pins in place Press both cables firmly into the two strain relief holes on the Dock Connector s front side fig 13 2 Turn the Remote Dock upside down You will see a male multi pin connector labeled Power Port and a female multi pin connector la beled Data Port fig 13 3 Conn...

Page 124: ...r end to either of the round connectors on the back of the next Remote Dock in the series and so on fig 13 4 When the RAD system has been completely set up connect the fan power supply s wall plug to a power source Operation The remote system is transparent to the base unit i e the Dock Connec tor allows the base to control the Alpha unit in the Remote Dock as if it were in the standard configurat...

Page 125: ...13 7 13 7 13 7 13 7 13 7 The Remote Alpha Dock System Figure 13 5 Flush mounting template ...

Page 126: ...he course of normal op eration to cause burns or cause liquids to boil explosively Wear safety goggles or other eye protection at all times during operation Warning Warning Warning Warning Warning The PTC 200 DNA Engine and PTC 225 DNA Engine Tetrad incorporate neu tral fusing which means that live power may still be available inside the ma chines even when a fuse has blown or been removed Never o...

Page 127: ...chines generate use and can radiate radiofrequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of these machines in a resi dential area is likely to cause harmful interference in which case the user will be required to correct the interference at his or her own expense In addition the PTC 200 DNA En...

Page 128: ...s and the holes or empty electron spaces in the P type blocks are ex cited at one conductor semiconductor interface which absorbs a small amount of heat The electrons and holes flow through the crystalline blocks and return to a low energy state at the other conductor semi conductor interface with the release of the previously absorbed heat A thermal gradient of up to 70 C can be generated across ...

Page 129: ......

Page 130: ... effect transistors The energy bursts are channeled into a high frequency transformer By changing the duration of the bursts that charge the transformer s magnetic core pulse width modulation a specific voltage output can be maintained even when the incoming voltage varies between 100 and 240 volts in the case of the DNA Engine Because the incoming power is being chopped so rapidly the incoming fr...

Page 131: ......

Page 132: ...upon arrival at our fac tory PLEASE ELIMINATE ALL BIOHAZARDS 3 Pack the machine in its original packaging If this has been misplaced or discarded call MJ RESEARCH to request shipment of packaging materials You can also request a loaner machine which will be provided if available a rental fee may apply You can use the loaner s packag ing to return the machine needing repair Remove the Alpha unit fr...

Page 133: ......

Page 134: ...nc is not responsible for special incidental or consequential damages resulting from any breach of warranty or under any other legal theory including downtime lost samples or experiments lost reagents lost profits goodwill damage to or replacement of equipment prop erty and any costs of recovering or reproducing experimental results and data Exclusions This warranty applies only to machines sold i...

Page 135: ...ove limitation or exclu sion may not apply to you This warranty gives you specific legal rights You may also have other rights depending upon your state of residence All provisions of this warranty are voided if the product is resold repaired or modified by any one other than MJ RESEARCH or an authorized distributor DNA Engine DNA Engine Tetrad Operations Manual E 2 ...

Page 136: ... T e m i T p m e T e m i T p m e T T E K U B E C I k c o l B 1 2 0 0 0 0 0 4 D N E N O I T A G I L k c o l B 1 2 0 0 0 0 0 5 1 D N E R H 1 7 3 k c o l B 1 2 3 0 0 0 0 1 7 3 0 0 0 0 0 4 D N E R H 6 7 3 k c o l B 1 2 3 0 0 0 0 6 7 3 0 0 0 0 0 4 D N E 5 6 k c o l B 1 2 0 0 0 0 0 5 6 D N E E R U T A N E D k c o l B 1 2 0 0 5 0 0 5 9 D N E L I O B k c o l B 1 2 0 0 5 0 0 0 0 1 D N E L L I K T U C k c o...

Page 137: ...g 4 3 D D D D D DNA Engine running protocols separately by block 12 7 simultaneosly on all blocks 12 8 DNA Engine Driver Software 9 4 DNA Engine Tetrad air supply requirements 12 6 Alpha units operating 12 7 cancelling protocol runs 12 8 cleaning 12 10 connecting power cables 12 5 environmental requirements 12 6 fuses changing 12 10 general information 12 2 installing 12 5 12 6 instant incubations...

Page 138: ...ration turning machine on 4 2 P P P P P Packing checklist 3 2 Passwords See Utilities files assigning password to folder Peltier effect C 1 Ports 4 3 IEEE 488 2 3 parallel printer 2 3 RS 232 2 3 Power Bonnet 2 4 Power cord location of jack 2 3 plugging in 3 2 Power supply requirements 3 3 acceptable power cords 3 3 Probe adding representative sample calculating amount of oil to add 4 12 choosing t...

Page 139: ...g 5 9 protocols adjusting for sample vessel type 4 6 R R R R R Remote Alpha Dock System air supply requirements 13 4 environmental requirements 13 3 installation 13 5 operation 13 6 packing checklist 13 3 power supply requirements 13 4 Robotics installation requirements 3 5 S S S S S Safety general instructions 1 3 guideline for safe use A 1 warnings A 1 Sample vessel selection chart 4 14 Sample v...

Page 140: ... Tetrad Operations Manual viewing a program in LCD window 8 6 list printing a program 8 7 setup 8 7 choosing a printer port 8 8 choosing a remote port 8 7 choosing a temperature control method for the Hot 8 9 determining software version number 8 9 ...

Page 141: ...ratories MODEL NUMBER PTC 200 YEARS OF MANUFACTURE 1997 and onward MJ RESEARCH INC as manufacturer of the equipment described above certifies that this model has been tested and conforms to the applicable Directives and Standards of the European Union EU as described above Test data to verify this conformity are available for inspection at either MJ RESEARCH INC or Finnzymes Oy at the addresses li...

Page 142: ...ample block heat pump subassemblies and one AT T RM2000 Power Supply YEAR OF MANUFACTURE 1996 MJ RESEARCH INC as manufacturer of the system described above certifies that this model has been tested and conforms to the applicable Directives and Standards of the European Union EU as described above Test data to verify this conformity are avail able for inspection at either MJ RESEARCH INC or Finnzym...

Page 143: ...ÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀÀ ÀÀÀÀÀ...

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