MJ Research PTC-0200 Operation Manual
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MJ Research PTC-0200 Operation Manual

Dna engine/dna engine tetrad
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PTC-0200 DNA Engine &
PTC-0225 DNA Engine Tetrad
Operations Manual
Version 4.0
M J R e s e a r c h
05434-05

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  • Page 1 @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ PTC-0200 DNA Engine & PTC-0225 DNA Engine Tetrad @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@ @@@@@...
  • 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 Copyright ©1999, MJ Research, Inc. All rights reserved. Reproduction in any form, either print or electronic, is prohibited without written permission of MJ Research, Inc. DNA Engine, DNA Engine Tetrad, Alpha, Hot Bonnet, Power Bonnet, Microseal, Chill-Out, Self- Seal and Twin Tower are trademarks of MJ Research, Inc.

  • Page 4: Table Of Contents

    Contents 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.

  • Page 5: Documentation Conventions

    Documentation Conventions Typographic Conventions The names of keyboard keys are set in sans serif type and encased in double angle brackets: Example Example Example Example Example «Proceed» Items in programming menus are italicized: Example Example Example Example 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:...

  • Page 6: Part I: The Dna Engine

    Part I The DNA Engine...

  • Page 8: Introduction

    Introduction Meet the DNA Engine, 1-2 Using This Manual, 1-2 Important Safety Information, 1-3...
  • Page 9 DNA Engine & DNA Engine Tetrad Operations Manual Meet the DNA Engine Thank you for purchasing an MJ R PTC-200 DNA Engine. De- ESEARCH signed by a team of molecular biologists and engineers, the DNA Engine will meet your needs for a versatile, easy-to-use, reliable, and compact programmable thermal cycler: •...
  • Page 10 Introduction • Chapter 10 explains the proper maintenance of the DNA Engine. • Chapter 11 offers troubleshooting information for the DNA Engine. • Chapter 12 describes the operation of the DNA Engine Tetrad. • Chapter 13 describes the operation of the RAD–0200 Remote Alpha Dock accessory.

  • Page 12: Layout And Specifications

    Layout and 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...
  • Page 13 DNA Engine & DNA Engine Tetrad Operations Manual Front View (Figure 2-1) Alpha unit, lid closed Thumbwheel Control panel Air exhaust vents (also on other side) Air intake vents Control Panel (Figure 2-2) Block key CAUTION:Sample blocks may be very hot ! ATTENTION: Les blocs peuvent etre tres chauds ! DNA Engine Block status lights...
  • Page 14 Layout and Specifications Back View (Figure 2-3) Alpha unit Air exhaust vents (also on other side) Alpha unit handle Air intake vents Power cord jack RS-232 port IEEE-488 port Parallel printer port Bottom View (Figure 2-4) Air intake vents Back Front...
  • Page 15 DNA Engine & DNA Engine Tetrad Operations Manual Alpha Units Single-Block Models 60V Alpha: Holds 60 x 0.5ml tubes 96V Alpha: Holds 96 x 0.2ml tubes or one 96-well microplate 192 Alpha: Holds one 192-well microplate 384 Alpha: Holds one 384-well microplate or one 96-well microplate Dual-Block Models 30/30 Dual Alpha:...
  • Page 16 Layout and Specifications Specifications Thermal range: –5˚ to 105˚C, but no more than 30˚C below ambient temperature ±0.3˚C of programmed target @ 90˚C, NIST-traceable Accuracy: ±0.4˚C well-to-well within 30 seconds of arrival at Thermal homogeneity: 90˚C (for most Alpha units; see specifications for in- dividual Alpha units) Up to 3˚C/sec for all single- and dual-block Alpha Ramping speed:...
  • Page 17 Gradient Specifications (96V Alpha module only) Accuracy: + 0.4°C of programmed target at end columns, 30 seconds after the 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...

  • Page 18: Installation

    Installation Packing Checklist, 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...
  • Page 19 DNA Engine & DNA Engine Tetrad Operations Manual Packing Checklist After unpacking the DNA Engine, check to see that you have received the following: • One DNA Engine base • One Alpha unit (more if additional units were ordered) • Two spare fuses •...
  • Page 20 Installation • Ambient temperature 5˚–31˚C • Relative humidity up to 90% • Unobstructed access to air that is 31˚C or cooler (see below) • Protection from excessive heat and accidental spills (Do not place the DNA Engine near such heat sources as radiators, and protect it from danger of having water or other fluids splashed on it, which can cause shorting in its electrical circuits.) Power Supply Requirements...
  • Page 21 DNA Engine & DNA Engine Tetrad Operations Manual • Do not allow dust or debris to collect in the air intake vents. The bottom air vents are particularly liable to collect dust and debris, sometimes completely clogging up. Check for dust and debris every few months, and clean the intake vents as needed.
  • Page 22 Installation Requirements for Robotics Installations Robotics installations require special attention to airflow and air tempera- ture. Typically in these installations, DNA Engines and other thermal cy- clers are crowded into a small area, along with other heat-generating equip- ment. Overheating can quickly occur when many of these machines are operating at once, unless preventive measures are taken.
  • Page 24 Operation Turning the DNA Engine On, 4-2 Understanding the Main Menu, 4-2 Using the Control Panel, 4-3 Operation Keys, 4-3 Status Indicator Lights, 4-3 Using the Data Ports, 4-3 Operating Alpha Units, 4-4 Installing an Alpha Unit, 4-4 Removing an Alpha Unit, 4-5 Opening an Alpha Unit, 4-5 Closing an Alpha Unit, 4-6 Selecting the Correct Sample Vessel, 4-6...
  • Page 25 DNA Engine & DNA Engine Tetrad Operations Manual Turning the DNA Engine On Move the power switch to “1” (the “On” position). In most The fan will turn on, and the power light on the keyboard will glow red. In most cases a self-test of the heat pumps will begin running (see note below).

  • Page 26: Operation

    Operation Using the Control Panel The control panel (see fig. 2-2) includes operation keys, status indicator lights, an LCD window for displaying programming and machine status text, and a numeric keypad for entering values into programs. Operation Keys • Select keys (left and right arrows): Move the cursor one space or op- tion to the left or right in the LCD window;...
  • Page 27 DNA Engine & DNA Engine Tetrad Operations Manual Operating Alpha Units Note: Note: Note: Note: Note: Operation of the Twin Tower will not be discussed, owing to the many differences between this type of Alpha unit and the others. Please see the Twin Tower Block Operations Manual for operating instructions.
  • Page 28 Operation Removing an Alpha Unit 1. Turn the DNA Engine off (see the Caution below). 2. Pull upward on the handle. When the lock releases, you will hear a click, and the Alpha unit will slide a little toward the back of the DNA Engine.
  • Page 29 DNA Engine & DNA Engine Tetrad Operations Manual Closing an Alpha Unit Press down on the top lever. The lever will close down over the thumbwheel as the Hot Bonnet closes down over the sample block. A click signifies that the Hot Bonnet’s latch has engaged.
  • Page 30 Operation X, for a description of Microseal ‘A’.) Thin-Walled Vs. Thick-Walled Tubes The thickness of sample tubes directly affects the speed of sample heat- ing and thus the amount of time required for incubations. Thick-walled tubes delay sample heating, since heat transfers more slowly through the tubes’...
  • Page 31 DNA Engine & DNA Engine Tetrad Operations Manual can be solidified at the end of a run. A pipette can then be used to pierce the wax in the tubes and remove the samples. The wax is dyed red to assist in monitoring its use.
  • Page 32 Operation material can interfere with the proper seating of a microplate or tubes, which would prevent the inner lid from exerting uniform pressure on the loaded microplate or tubes. 2. Open the Hot Bonnet. Turn the blue thumbwheel all the way counter- clockwise to completely raise the inner lid.
  • Page 33 DNA Engine & DNA Engine Tetrad Operations Manual Hot Bonnet’s Lid Pressure,” p. 4-8). To ensure uniform heating and cooling of samples, sample vessels must be in complete contact with the block. Adequate contact is ensured by always doing the following: •...
  • Page 34 Operation ever possible, use high-quality thin-wall tubes intended for thermal cycling (see chapter appendix 4-A for a tube and plate selection chart). Using the Optional Probe The probe consists of a precision thermistor mounted in a thin-walled plastic tube. A thin wire, encased in a small plastic tube, runs from the thermistor to the probe’s plug, which is inserted into a slot at the back of the Alpha unit (fig.
  • Page 35 DNA Engine & DNA Engine Tetrad Operations Manual Adding the Oil Viscous oils are the best choice for the probe tube’s representative sample. They closely mimic the thermal characteristics of buffer solu- tion, which changes temperature sluggishly due to the high specific heat of water.
  • Page 36 Operation Do not use paraffin wax or Chill-out liquid wax, or the probe readings will not be accurate. Caution: Caution: Caution: Caution: Caution: Do not use water, saline, or any other aqueous solution as a representative sample. Aqueous solutions will de- stroy the thermistor.
  • Page 37 Appendix 4-A Tube, Microplate, and Sealing System Selection Chart Reaction vessel fits block without modification. ❍ Reaction vessel must be cut to fit this block. - l i i r c i t p - f l i l s s - F i r e ❍...
  • Page 38 Appendix 4-B Safety Warning Regarding Use S Nucleotides Some researchers have experienced a problem with radioactive contamination when using S in thermal cyclers. This problem has occurred with all types of reaction vessels. The Problem When S nucleotides are thermally cycled, a volatile chemical breakdown product forms, prob- ably SO .
  • Page 39 Operation appropriate detection methods and cleaning procedures for this isotope. Consult your radia- tion safety officer for his or her recommendations. If mild cleaning agents do not remove radioactivity, harsher cleaners may be used. Users have suggested the detergent PCC-54 (Pierce Chemical Co., Rockford, Illinois; Pierce Eurochemie B.V., Holland), Micro Cleaning Solution (Cole-Parmer, Niles, Illinois), and Dow Bathroom Cleaner (avail- able in supermarkets).
  • Page 40 Appendix 4-C Using Silicone Oil in the Probe Tube The following light and heavy silicone oils may be used instead of mineral oil as the representa- tive sample in a probe tube: • Dow Corning #200 light silicone oil (dimethypolysiloxane, Sigma #DMPS-5X) Density: 0.97g/ml Viscosity: 50cs Volume to use: 1.7 x volume of buffer in individual sample tube, plus one volume of oil overlay.
  • Page 41 Running Protocols Running a Protocol, 5-2 Choosing a Stored Protocol to Run, 5-2 Choosing a Block to Run the Protocol On, 5-3 Setting Up the Temperature Control Method, 5-3 Setting Up a Block-Control Protocol, 5-3 Setting Up a Calculated-Control 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...

  • Page 42: Running A Protocol

    DNA Engine & DNA Engine Tetrad Operations Manual Running a Protocol Running a protocol on the DNA Engine involves three steps: 1. Choosing a stored protocol to run 2. Choosing a block to run it on, if a dual-block Alpha unit is installed 3.

  • Page 43: Running Protocols

    Running Protocols In either instance, after you press «Proceed», a screen similar to the fol- lowing example will be displayed: Run: 2-STEP Vessel Type: _TUBES Plate The top line of the screen will identify the selected protocol (2-STEP in the example). The other lines on the screen will request information needed to set up the temperature control method (explained below).

  • Page 44: Setting Up A Calculated-Control Protocol

    DNA Engine & DNA Engine Tetrad Operations Manual Select Yes or No, then press «Proceed». The protocol will begin running. Setting Up a Calculated-Control Protocol Three screens will be presented: • A screen asking for sample vessel information: Run: 2-STEP Vessel Type: _TUBES Plate...

  • Page 45: Setting Up A Probe-Control Protocol

    Running Protocols Setting Up a Probe-Control Protocol A single screen asking about use of the heated lid will be displayed. Se- lect Yes or No, then press «Proceed». If the probe is installed, the probe verification screen will be displayed: Run: PROBE1 PROBE control: Verify probe ready...

  • Page 46: Switching Between The Runtime Screen And The Main Menu

    DNA Engine & DNA Engine Tetrad Operations Manual hand corner of the screen. The first digit is the minutes elapsed; the two digits after the colon are the seconds elapsed. For protocols using calculated control or probe control, press the left «Se- lect»...
  • Page 47 Running Protocols Printing a Log for a Running Protocol If the DNA Engine is connected to a printer, you can print a log for the run that includes • The DNA Engine’s serial number and software version • The protocol’s name •...

  • Page 48: Manually Stepping Through A Protocol

    DNA Engine & DNA Engine Tetrad Operations Manual Manually Stepping Through a Protocol Once a protocol is running, pressing «Proceed» gives you the option of immediately advancing the protocol to the next programmed step, even if the machine is currently ramping the block’s temperature (see chapter 6 for information on ramping).

  • Page 49: Resuming A Protocol After A Power Outage

    Running Protocols Select Yes, then press «Proceed» to cancel the protocol. The total run time for the protocol will be displayed: Run: 2-STEP PROGRAM CANCELED Total time: 1:15 Press «Proceed» to return to the Main Menu. Note: Note: Note: Note: Note: Turning off the machine does not stop a running protocol.

  • Page 50: Using The Instant Incubation Feature

    DNA Engine & DNA Engine Tetrad Operations Manual Using the Instant Incubation Feature The DNA Engine may be converted to a constant-temperature incubator by pressing «Instant Incubate». A screen allowing use of the heated lid will be displayed: INCUBATE: Use heated lid? Use the «Select»...
  • Page 51 Creating Programs The Elements of a Program, 6-2 Designing a New Program, 6-2 Translating a Protocol into a Program, 6-2 Using the GoTo Step to Write Short Programs, 6-3 Choosing a Temperature Control Method, 6-3 Calculated Control, 6-4 Block Control, 6-4 Probe Control, 6-4 Modifying Block- and Probe-Control Programs for Calculated Control, 6-5 Modifying a Program Designed for a Different Machine, 6-5...

  • Page 52: The Elements Of A Program

    DNA Engine & DNA Engine Tetrad Operations Manual The Elements of a Program DNA Engine programs consist of a series of steps encoding a protocol. These steps are run using one of three possible temperature control meth- ods: calculated control, block control, and probe control. Programs may contain five types of steps.

  • Page 53: Creating Programs

    Creating Programs Designing a New Program Translating a Protocol into a Program Until you are completely familiar with programming the DNA Engine, you may find it helpful to first translate the protocol into DNA Engine program steps and options on paper. Write down the protocol to be pro- grammed, one step per line.

  • Page 54: Calculated Control

    DNA Engine & DNA Engine Tetrad Operations Manual at programmed temperatures. This includes optimized “overshoots” of the block by a few degrees for a few seconds, which bring the samples to the programmed temperatures. • Block control: The DNA Engine adjusts the block’s temperature to maintain the block at programmed temperatures, independent of sample temperature.

  • Page 55: Probe Control

    Creating Programs Probe Control Probe control is available for unusual circumstances that may require it. Ordinarily, though, it should be used with caution. While the DNA En- gine will have no trouble heating the probe to the target temperature, if the probe is seated or prepared differently from the sample tubes, actual sample temperatures can vary widely from the probe’s temperature.

  • Page 56: Initiating The Program

    DNA Engine & DNA Engine Tetrad Operations Manual Initiating the Program To initiate a new program, select Enter from the Main Menu, then press «Proceed». A naming screen will be displayed: Enter: Name: A Naming the Program Name the program an eight-character word consisting of any combina- tion of letters (Roman and Greek), numbers, punctuation marks, or Japa- nese Katakana.

  • Page 57: Entering A Temperature Step

    Creating Programs Enter: CUSTOM1 Step 1= _TEMP Gradient Ramp Use this menu to enter each step of the program: • Temp enters a temperature step. • Gradient enters a Gradient step. • GoTo enters a GoTo step (note: since a protocol can not begin with a GoTo step,GoTo does not appear on the initial Enter Menu).

  • Page 58: Entering A Gradient Step

    DNA Engine & DNA Engine Tetrad Operations Manual low): Enter: CUSTOM1 1= 92.0˚ Time: Note: Note: Note: If a hold time of zero (0) is entered, the DNA Engine will hold the Note: Note: block at the target temperature indefinitely. Press «Proceed».
  • Page 59 Creating Programs The gradient screen will appear: Enter: CUSTOM1 Lower Temp ° C: Enter the lower limit temperature (for the purposes of this example, 50°), then press «Proceed». The upper temperature screen will appear: Enter: CUSTOM1 50.0° Upper Temp ° C: Enter the upper temperature (for the purposes of this example, 70°), then press «Proceed».

  • Page 60: Editing A Gradient Step

    DNA Engine & DNA Engine Tetrad Operations Manual Editing a gradient step To edit a gradient step, select Edit from the Main Menu. The program will be displayed as follows: List: CUSTOM1 1= 92.0° for 0:20 2= 50.0° to 70.0° for 0:30 Use the «Select»...
  • Page 61 Creating Programs List: Programs _GRADIENT CALCULATOR Select Gradient Calculator and press the «Proceed» key : Lower Temp ° C: 50.0° Upper Temp ° C: 70.0° Enter lower limit temperature of the gradient using the number keys and then press the «Proceed» key. Enter the upper temperature for the gradient using the number keys and «Proceed»...

  • Page 62: Entering A Ramp Step

    DNA Engine & DNA Engine Tetrad Operations Manual Entering a Ramp Step To enter a ramp step, select Ramp from the Enter Menu. The first Ramp screen will be displayed: Enter: CUSTOM1 Rate ˚C / s: _ The second line of this screen shows the number of the step being pro- grammed (3 is used in the example above).

  • Page 63: Entering A Goto Step

    Creating Programs Enter: CUSTOM1 3= 2.0˚/s to 69.0˚ OK? _YES Option 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. •...

  • Page 64: Entering The End Step

    DNA Engine & DNA Engine Tetrad Operations Manual Press «Proceed». The step number will move to the second line of the screen, and a line allowing an additional number of cycles to be entered will be displayed: Enter: CUSTOM1 3=GoTo 1 Addtnl cycles: Enter the additional number of times the program should cycle back to the step (3 is used in the example below):...

  • Page 65: Modifying A Program Step With The Options

    Creating Programs Select one of the displayed choices, then press «Proceed»: • Yes accepts the step, stores the program, and displays the Main Menu. • No displays the Enter Menu so that additional steps can be added. If you have created custom folders for your programs (see chapter 8), choosing Yes brings up a screen listing the folders: Save program in: <MAIN>...

  • Page 66: Entering An Extend Option

    DNA Engine & DNA Engine Tetrad Operations Manual played: Enter: CUSTOM1 92.0˚ for 0:30 ˚C / cycle: The temperature step being modified appears on the second line of this screen. The plus sign on the third line means that the screen is set up to enter a progressive increase in temperature per cycle.

  • Page 67: Entering An Beep Option

    Creating Programs As for Inc, the temperature step being modified appears on the second line of this screen. The plus sign on the third line means that the screen is set up to enter progressive lengthening of hold time. Press «–» to switch to a minus sign, allowing entry of a progressive shortening of hold time.

  • Page 68: Revising During Programming

    DNA Engine & DNA Engine Tetrad Operations Manual the Enter Menu to enter the next step in the program. • No cancels the Beep option. • Option displays the Options Menu again, if a temperature step is being modified. Use the Options Menu to enter another option for the step.

  • Page 69: Deleting A Program

    Creating Programs At this point, you can choose to change selected values in program steps, to add an option, to enter Edit mode, or to delete the entire program. Press the «Select» keys to scroll through the program. The left «Select» key moves the cursor backward through the steps, and the right «Se- lect»...
  • Page 70 DNA Engine & DNA Engine Tetrad Operations Manual values, deleting them as it goes. When all values have been deleted, keep pressing «Cancel» to move backward through Enter mode screens until the Main Menu reappears, at which point you 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.

  • Page 71: Editing Programs

    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...
  • Page 72 DNA Engine & DNA Engine Tetrad Operations Manual Editing a Stored Program The DNA Engine’s editing tools, available through Edit on the Main Menu, make it easy to extensively edit stored programs by • Changing individual values in program steps, •...
  • Page 73 Editing Programs ✔ Tip: Tip: Tip: Tip: Tip: To retain the original version of a program, copy the program (see “Copying a Program,” chapter 8), and then edit the copy. Editing the Program The first editing screen displays all three temperature control methods. The program’s current temperature control method is displayed in all- capital letters: Edit: CUSTOM1...
  • Page 74 DNA Engine & DNA Engine Tetrad Operations Manual Inserting a New Step To insert a new step, select Insert from the Edit Menu, then press «Pro- ceed». The Enter Menu will be displayed for the new step (a new step 2 is added in the example below): Edit: CUSTOM1 Step 2= _TEMP...
  • Page 75 Editing Programs press «Proceed». A line allowing the editing session to be ended will be displayed on the last line of the screen: Edit: CUSTOM1 2=End Step: _END Insert • End saves the changes and displays the Main Menu. This ends the editing session.
  • Page 77 Using the Utilities Locating a Stored Program, 8-2 File Utilities, 8-2 Creating a Folder, 8-3 Assigning a Password to a Folder, 8-3 Deleting a Folder, 8-4 Copying a Program, 8-4 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...
  • Page 78 DNA Engine & DNA Engine Tetrad Operations Manual Locating a Stored Program Many of the DNA Engine’s utilities require you to locate a program stored in the machine. The actions necessary to do this depend on whether your programs have been stored in the <MAIN> folder or in custom folders. •...

  • Page 79: Using The Utilities

    Using the Utilities Creating a Folder The DNA Engine’s memory can hold up to 11 folders, including the <MAIN> folder. New programs are placed in the <MAIN> folder by de- fault unless a different folder is specified. To create a folder, select Folder from the Files Menu, then press «Pro- ceed».
  • Page 80 DNA Engine & DNA Engine Tetrad Operations Manual Passwords can be changed at any time. Follow the steps described above to select the desired folder, then press «Proceed». A screen asking for the old password will be displayed: Secure: <FOLDER1> Old password: _ Enter the old password, then press «Proceed».
  • Page 81 Using the Utilities Select a folder to copy the program to, then press «Proceed». A naming screen will be displayed: Copy CUSTOM1 to: New name: A Name the copied program (see “Naming the Program,” chapter 6), then press «Proceed». The program will be copied to the specified folder un- der the new name, and the Main Menu will be displayed.
  • Page 82 DNA Engine & DNA Engine Tetrad Operations Manual Select Yes, then press «Proceed». The program will be deleted, and the Main Menu will be displayed. To cancel the deletion, press «Cancel», or select No and press «Pro- ceed». List Utilities Use these utilities, available under List, to accomplish the following task: •...
  • Page 83 Using the Utilities Printing a Program First ensure that the DNA Engine is connected to a printer. If no printer is connected, you will not be given the option of printing at all. The DNA Engine’s parallel interface is compatible with most serial and laser printers, the Epson®...
  • Page 84 DNA Engine & DNA Engine Tetrad Operations Manual The cursor will be positioned at the port currently in use. To choose the serial port, select Serial, then press «Proceed». The cursor will move to Serial, and a line allowing a baud rate to be specified will be displayed on the last line of the screen: Printer: _SERIAL...
  • Page 85 Using the Utilities Choosing a Minimum Block Temperature for the Hot Bonnet To set a minimum block temperature below which the Hot Bonnet will automatically turn off, select Lid from the Setup Menu, then press «Pro- ceed». The following screen will be displayed: Lid: Mode _MINIMUM...
  • Page 86 DNA Engine & DNA Engine Tetrad Operations Manual The mode currently in use will be selected in the screen; select a different control mode if desired, then press «Proceed» to enter the mode and re- turn to the main menu. If the tracking mode is chosen, a lid offset (up to 45˚C above the block, but not to exceed 110˚C) must be specified.

  • Page 87: Networking

    Networking Overview of Networking, 9-2 Networking Machines Without 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...

  • Page 88: Overview Of Networking

    DNA Engine & DNA Engine Tetrad Operations Manual Overview of Networking Up to 15 machines consisting of any combination of DNA Engines and DNA Engine Tetrads may be networked, with or without a computer as the controller. When networking with a computer, all the machines are controlled from the computer’s keyboard.

  • Page 89: Running A Protocol On Networked Machines

    Networking Select IEEE-488, then press «Proceed». The remote addressing screen will be displayed: Remote: Serial _IEEE-488 Address (0-30): 0 Enter an address number for the machine. Set the controller DNA Engine’s address to 0. Give the other machines in the network any number from 1 to 30.

  • Page 90: Networking Machines With A Computer

    DNA Engine & DNA Engine Tetrad Operations Manual The machine’s address number will be identified in the upper right-hand corner of the screen. “Remote” indicates that this is the network screen for a slave unit, and “60V” indicates the type of Alpha unit that has been selected.

  • Page 91: Creating A Computer-Controlled Ieee-488 Network

    Networking may be used to write your own driver software. A computer-controlled network can be connected via IEEE-488 cables or RS-232 (serial) cables. In either case, the computer acts as the controller of the network and uses the driver software to communicate with the networked machines.

  • Page 93: Maintenance

    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 10-1 10-1 10-1 10-1 10-1...
  • Page 94 DNA Engine & DNA Engine Tetrad Operations Manual Cleaning the DNA Engine Cleaning the Chassis and Block Clean the outside of the DNA Engine and Alpha unit with a damp, soft cloth or tissue whenever something has been spilled on it or the chassis is dusty.
  • Page 95 Maintenance Cleaning Radioactive or Biohazardous Materials Out of the Block When cleaning machines that have been running radioactive or biohaz- ardous reactions, consult your institution’s radiation safety officer or biosafety officer regarding cleaning methods, monitoring, and dispos- ing of contaminated materials. Changing the Fuses The circuits in the DNA Engine are protected by two fuses (6.3A fast- acting, 5 x 20mm).

  • Page 97: Troubleshooting

    Troubleshooting Error Messages, 11-2 Problems Related to Protocols, 11-6 Problems Related to Environmental Conditions, Setup, and Maintenance, 11-8 11-1 11-1 11-1 11-1 11-1...
  • Page 98 DNA Engine & DNA Engine Tetrad Operations Manual Error Messages Note: The DNA Engine/Tetrad software is highly sensitive with re- spect to block and heat-sink errors. When such errors messages occur, try restarting the protocol. If the message fails to reappear, proceed as usual.
  • Page 99 Troubleshooting , t l . t e . e l , t l e l i , r i ° 1 ° 1 , s t t s i - i s s t i s t i C û c i t "...
  • Page 100 DNA Engine & DNA Engine Tetrad Operations Manual , t l , y l i t s , t l , t l , t l , t l . f f l l i l i a . s l s t i , y l l l a...
  • Page 101 Troubleshooting , r i ° 1 ° 1 P " P " " . " . , t l l l i l l i l l i l i t ° 1 , r i ° 1 l l i l l i l i t - f l...
  • Page 102 DNA Engine & DNA Engine Tetrad Operations Manual Problems Related to Protocols Following is a general description of some common problems related to the protocols and reaction components in sequencing and amplification applications. For a more detailed discussion of protocols and reactions, see Current Protocols in Molecular Biology (F.
  • Page 103 Troubleshooting t s i i l i s ' l > t s i i l i l i f l l i . l i S " " e t i f s l l 11-7 11-7 11-7 11-7 11-7...
  • Page 104 DNA Engine & DNA Engine Tetrad Operations Manual Problems Related to Environmental Conditions, Setup, and Maintenance . r i , t s , s i S " " " " , t " " g - i s i t r <...

  • Page 105: Part Ii: The Dna Engine Tetrad

    Part II The DNA Engine Tetrad...

  • Page 107: Information Specific To The Dna Engine Tetrad

    Information Specific to the DNA Engine Tetrad Meet the DNA Engine Tetrad, 12-2 Specifications, 12-2 Layout, 12-3 Front View, 12-3 Control Panel, 12-3 Back View, 12-4 Bottom View, 12-4 Unpacking and Installing the DNA Engine Tetrad, 12-5 Packing Checklist, 12-5 Installation, 12-5 Connecting the Cables, 12-5 Power Supply Requirements, 12-6...

  • Page 108: Meet The Dna Engine Tetrad

    DNA Engine & DNA Engine Tetrad Operations Manual Meet the DNA Engine Tetrad The DNA Engine Tetrad harnesses four DNA Engines in a single com- pact machine. Four Alpha units of any type can be loaded into the DNA Engine Tetrad base, one unit into each “quadrant” of the base. The same factory-installed and custom protocols can be run on the DNA Engine Tetrad as on the DNA Engine.

  • Page 109: Layout

    Information Specific to the DNA Engine Tetrad Layout Front View (Figure 12-2) Dual-block Alpha unit Single-block Alpha unit Power supply Power supply air intake vent Tetrad base Front air exhaust vents Control panel Control Panel (Figure 12-3) Instant Block status incubation lights LCD display...

  • Page 110: Back View

    DNA Engine & DNA Engine Tetrad Operations Manual Back View (Figure 12-4; Alpha units removed) Tetrad base Power supply Power supply air exhaust vents RS-232 Cables plug port in here Parallel IEEE-488 printer port port Signal cable Electrical outlet plug Power cable Bottom View (Figure 12-5)

  • Page 111: Unpacking And Installing The Dna Engine Tetrad

    Information Specific to the DNA Engine Tetrad Unpacking and Installing the DNA Engine Tetrad Packing Checklist After unpacking the DNA Engine Tetrad, check to see that you have received the following: • DNA Engine Tetrad base • Four Alpha units •...

  • Page 112: Power Supply Requirements

    DNA Engine & DNA Engine Tetrad Operations Manual The signal and power cables terminate in twist-lock plugs. To screw a plug in, first make sure the power supply is not plugged into an outlet. Press the plug into the socket, and twist it to the right. A snap will be felt when the plug completely seats in the socket;...

  • Page 113: Operating The Dna Engine Tetrad

    Information Specific to the DNA Engine Tetrad of the air exhaust vents on the front and back of the DNA Engine Tetrad (fig. 12-2). These screws may be replaced with longer ones, as long as they are M4 x 0.7 screws. Operating the DNA Engine Tetrad Turning the DNA Engine Tetrad On First, make sure Alpha units are installed in all four quadrants.

  • Page 114: Running The Same Protocol On All Blocks

    DNA Engine & DNA Engine Tetrad Operations Manual When the desired block has been selected, press «Proceed» to run the protocol. Note: To run different protocols concurrently, press «Block» to return to the main screen, and select a new protocol and a new block as de- scribed in this section.

  • Page 115: Programming The Dna Engine Tetrad

    Information Specific to the DNA Engine Tetrad Select Yes, then press «Proceed». A screen announcing the cancellation and citing the total time for the run will be displayed: Run: 2-STEP on 2B PROGRAM CANCELED Total time: 1:10 Programming the DNA Engine Tetrad The DNA Engine Tetrad is programmed in the same way as the DNA Engine (see chapter 6).

  • Page 116: Troubleshooting The Dna Engine Tetrad

    DNA Engine & DNA Engine Tetrad Operations Manual Troubleshooting the DNA Engine Tetrad The Tetrad is subject to the same problems with operations, protocols, and reaction results as the DNA Engine (see chapter 11). Maintaining the DNA Engine Tetrad Cleaning Clean the DNA Engine Tetrad according to the instructions in chapter 10 for cleaning the DNA Engine.

  • Page 117: Part Iii: Accessories

    Part III Accessories...

  • Page 119: The Remote Alpha Dock System

    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 13-1 13-1 13-1 13-1 13-1...
  • Page 120 About the Remote Alpha Dock System The Remote Alpha Dock system is designed to add flexibility to the in- stallation and operation of the MJ Research PTC-200 DNA Engine and PTC-225 DNA Engine Tetrad. The system allows Alpha units to be placed at a distance from the PTC-200 or PTC-225 base, enabling more efficient use of space and facilitating robotic operation.
  • Page 121 Environment The Remote 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...
  • Page 122 DNA Engine & DNA Engine Tetrad Operations Manual • Remote Docks with mounted Alpha units may be stacked vertically as long as a minimum bottom clearance is maintained that would be no less than that resulting from the unit being placed on a solid hori- zontal platform.
  • Page 123 The Remote Alpha Dock System Installation • Turn the Dock Connector upside down, so that the green circuit board is visible. Check that the ground lead remains attached at both ends (fig. 13-1). Note the two female multi-pin sockets, one labeled “DATA,”...
  • Page 124 DNA Engine & DNA Engine Tetrad Operations Manual • Attach the wall-plug power cord to the fan power supply. • Attach the fan power supply’s round jack to either of the round con- nectors on the back of the Remote Dock (fig. 13-4). •...
  • Page 125 The Remote Alpha Dock System Figure 13-5 Flush-mounting template 13-7 13-7 13-7 13-7 13-7...

  • Page 126: Appendix A: Safety Warnings And Guidelines

    Appendix A Safety Warnings and Guidelines Warning: Warning: Warning: Warning: Warning: Operating the PTC-200 DNA Engine or PTC-225 DNA Engine Tetrad before reading this manual can constitute a personal injury hazard. Only qualified laboratory personnel trained in the safe use of electrical equipment should op- erate these machines.
  • Page 127 DNA Engine & DNA Engine Tetrad Operations Manual • Ambient temperature 5˚–31˚C • Maximum relative humidity 90%, noncondensing • Transient overvoltage per Installation Category II, IEC 664 • Pollution degree 2, in accordance with IEC 664 Electromagnetic Interference The PTC-200 DNA Engine and PTC-225 DNA Engine Tetrad have been tested and found to com- ply with the limits for a Class A digital device, pursuant to part 15 of the US FCC Rules.

  • Page 128: Appendix B: How A Peltier Heat Pump Works

    Appendix B How a Peltier Heat Pump Works The functional heart of every DNA Engine is a high-performance Peltier-effect heat pump (also known as a “thermoelectric module”). This solid-state device is manufactured to withstand the thermal stresses associated with rapidly cycling temperatures. A thermoelectric module consists of numerous pairs Figure A-1 A thermoelectric module.

  • Page 130: Appendix C: How A Switching Power Supply Works

    Appendix C How a Switching Power Supply Works Almost all solid-state electronic devices, including the DNA Engine’s thermoelectric module, re- quire direct current (DC) for operation. However, electric utilities supply low-Hertz alternating current (AC), which varies in voltage and frequency from nation to nation. The DNA Engine uses switching transistors, combined with high-frequency, resonant transformers, to convert the in- coming AC to DC.

  • Page 132: Appendix D: Shipping Instructions For Us Residents

    4. Write the RMA number on the outside of the box. 5. Ship the machine (freight prepaid) to the following address. We recommend you purchase insurance from your shipper. Ship to: Repair Department MJ Research, Inc. 136 Coolidge Ave. Watertown, MA 02172...

  • Page 134: Appendix E: Warranties

    Warranties U.S. Domestic Warranty, Standard MJ R , Inc. warrants NEW MJ RESEARCH BRAND THERMAL CYCLERS (MODELS PTC- ESEARCH 100, PTC-150, PTC-200 & PTC-225) against defects in material and workmanship for a period of two years from the date of purchase. If a defect is discovered, MJ R , Inc.
  • Page 135 DNA Engine & DNA Engine Tetrad Operations Manual Some states OF THE U.S.A. do not allow the exclusion or limitation of incidental or consequential damages or limitations on how long an implied warranty lasts, so the above limitation or exclu- sion may not apply to you.

  • Page 136: Appendix F: Factory-Installed Protocols

    Appendix F: Factory-Installed Protocols Appendix F Factory-Installed Protocols Note: A programmed time of 0:00:00 means “hold at this temperature forever.” l o r t l o r t l o r t l o r t l o r t a N e m a N e m a N e m...

  • Page 137: Index

    Index A A A A A separately by block 12-7 simultaneosly on all blocks 12-8 Accessories. See Power Bonnet DNA Engine Driver Software 9-4 Air supply requirements DNA Engine Tetrad ensuring adequate air supply 3-3 air supply requirements 12-6 Ensuring air is cool enough 3-4 Alpha units, operating 12-7 troubleshooting problems with 3-4 cancelling protocol runs 12-8...
  • Page 138 DNA Engine & DNA Engine Tetrad Operations Manual F F F F F O O O O O FCC warning A-2 Oil, use of in block. See Sample vessels Fuses Operation changing 10-3 turning machine on 4-2 H H H H H P P P P P Hot Bonnet Packing checklist 3-2...
  • Page 139 Index S S S S S Naming a program 6-6 revising during 6-14 Safety setting a lengthy hold time 6-7 general instructions 1-3 Programs guideline for safe use A-1 designing 6-2–6-5 warnings A-1 choosing temperature control method. See Sample vessel Temperature control methods selection chart 4-14 translating protocol into programinto pro-...
  • Page 140 DNA Engine & DNA Engine 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 In-4 In-4...
  • Page 141 “CE” M ECLARATION OF ONFORMITY TO PPLY MJ R . hereby declares that the MJ R PTC-200 ESEARCH ESEARCH DNA Engine™ thermal cycler conforms to the following directives and standards: : 89/336/EEC & 73/23/EEC PPLICATION OF OUNCIL IRECTIVES : EN55011; EN50082-1; TANDARDS TO HICH ONFORMITY IS...
  • Page 142 ECLARATION OF ONFORMITY MJ R . hereby declares that the MJ R PTC-225 DNA Engine ESEARCH ESEARCH Tetrad™ thermal cycling system conforms to the following directives and standards: : 89/336/EEC PPLICATION OF OUNCIL IRECTIVES : EN55011 & EN50082-1 TANDARDS TO HICH ONFORMITY IS ECLARED...
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