MJ Research DNA Engine Dyad PTC-220 User manual

PTC-220 DNA Engine Dyad™
Peltier Thermal Cycler
Operations Manual
Version 1.3
Boston • San Francisco • Tahoe • Copenhagen • Seoul
i

Copyright ©2002, MJ Research, Incorporated. All rights reserved. Reproduction in any form,
either print or electronic, is prohibited without written permission of MJ Research, Incorporated.
05570 revA.A
DNA Engine, DNA Engine Tetrad, DNA Engine Dyad, Dyad, Alpha, Hot Bonnet, Power Bonnet,
Multiplate, Chill-out, Self-Seal, Remote Alpha Dock, MJ Research marks and helix logo are trade
and/or service marks belonging to MJ Research, Incorporated.
Microseal, Hard-Shell, and Twin Towers are registered trademarks belonging to MJ Research,
Incorporated.
Datalight is a registered trademark of Datalight, Inc. ROM-DOS is a trademark of Datalight, Inc.
WinLight is a trademark of Datalight, Inc. Copyright 1989-2000 Datalight, Inc., All Rights
Reserved.
Thermal cyclers can be used for a number of purposes, including the polymerase chain reaction
(PCR). PCR is covered by patents owned by Hoffmann-La Roche, Inc., and F. Hoffmann-La Roche,
Ltd., who have granted exclusive and nonexclusive licenses for some types of applications.
Roche and its licensees provide end-user licenses within their respective fields. These licenses
have different 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 below:
In the United States: In other nations:
Licensing Manager PCR Licensing Manager
Roche Molecular Systems, Inc. F. Hoffmann-La Roche Ltd.
1145 Atlantic Avenue Building 222/350
Alameda, CA 94501 USA CH-4002 Basel, Switzerland
(510) 814-2970 41-61-687-3031
Fax: (510) 814-2977 Fax: 41-61-687-2113
ii

Contents
Documentation Conventions....................................................................... iv
Part I: The DNA Engine Dyad Thermal Cycler
Introduction ........................................................................................ 1-1
Layout and Specifications..................................................................... 2-1
Installation.......................................................................................... 3-1
Operation .......................................................................................... 4-1
Creating Programs .............................................................................. 5-1
Managing and Editing Programs........................................................... 6-1
Running Programs ............................................................................... 7-1
Using the Utilities ................................................................................ 8-1
Maintenance ...................................................................................... 9-1
Troubleshooting .................................................................................. 10-1
Part II: Accessories
Alpha Units and the Remote Alpha Dock System ..................................... 11-1
Appendix A: Safety Warnings and Guidelines ............................................. A-1
Appendix B: How a Peltier Heat Pump Works .............................................. B-1
Appendix C: Shipping Instructions for US Residents ...................................... C-1
Appendix D: Warranties .......................................................................... D-1
Index ...................................................................................................... In-1
Declaration of Conformity.......................................................................... DoC-1
iii

Documentation Conventions
Before describing the various features of the Dyad cycler, let’s define some “common ground”
conventions.
• << >> will be used to indicate actual keys on the control panel, such as <<ENTER>>,
<<1>> and <<LEFT>>.
• < > will be used to indicate windowed menu items or buttons, such as <PROGRAMS>,
<RUN> and <TOOLS>.
•
Italics
will be used to indicate windowed items that are not drop down menu items or
buttons, such as
Calculated
,
Block
, and
Tracking
. Typically, these will be parameter
selection items.
•
Select
is meant to be synonymous with
click on
,
point-and-click
, and any phraseol-
ogy implying selection of menu or option items with a mouse. Particularly with the Dyad
cycler,
select
should symbolize any physical selection on the Dyad input devices (touch
pad/mouse, numeric keypad, arrow keys) to access one of the user interface windows.
This includes single or double taps on the touch pad, pressing of the left touch pad
button, or pressing the <<Enter>> button on the numeric keypad.
iv

Introduction
1
Meet the DNA Engine Dyad Cycler, 1-2
Using This Manual, 1-2
Important Safety Information, 1-3

1-2
DNA Engine Dyad Operations Manual
Meet the DNA Engine Dyad Cycler
Thank you for purchasing an MJ Research DNA Engine Dyad™thermal cycler. Designed by
a team of molecular biologists and engineers, the DNA Engine Dyad cycler delivers multi-
block thermal cycling with superior thermal performance. The programmable Dyad™cycler,
with its dual-bay chassis, is ideal for running multiple protocols and accommodating multiple
users. Some of the Dyad cycler’s many features include:
•Interchangeable sample blocks—the Alpha™unit family accommodates a vari-
ety of tubes, microplates, and slides
•Hot Bonnet™heated lid for oil-free cycling or the Power Bonnet™lid for auto-
mated systems
•Intuitive software with user-friendly interface for programming, editing, file man-
agement, and much more
•Choice of calculated temperature control for highest speed and accuracy, or of
block or probe temperature control for compatibility with protocols designed for
a variety of instrument types
•Instant Incubate feature for continuous-temperature incubations
Using This Manual
This manual contains instructions for operating your DNA Engine Dyad cycler safely and
productively:
•Chapter 2 acquaints you with the physical characteristics of the DNA En-
gine Dyad cycler.
•Chapters 3–4 present the basics of installation and operation for the DNA
Engine Dyad cycler.
•Chapters 5, 6 and 7 describe the creation, editing and running of pro-
grams.
•Chapter 8 outlines the software utilities.
•Chapter 9 explains the proper maintenance of the DNA Engine Dyad cycler.
•Chapter 10 offers troubleshooting information for the DNA Engine Dyad cy-
cler.
•Chapter 11 describes the installation and operation of the RAD-200
Remote Alpha Dock™ accessory.

1-3
Introduction
Important Safety Information
Safe operation of the DNA Engine Dyad cycler begins with a complete understanding of
how the instrument works. Please read this entire manual before attempting to operate the
Dyad cycler. Do not allow anyone who has not read this manual to operate the instrument.
Warning: The DNA Engine Dyad cycler can generate enough heat to inflict serious
burns and can deliver strong electrical shocks if not used according to the
instructions in this manual. Please read the safety warnings and guide-
lines in Appendix A, and exercise all precautions outlined in them.
Warning: Do not block the Dyad cycler’s air vents (see figs. 2-1 and 2-4 for loca-
tion). Obstructing air vents can lead to overheating and slightly enhanced
risk of electrical shock and fire.

1-4
DNA Engine Dyad Operations Manual

Layout and
Specifications
2
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, 2-5

2-2
DNA Engine Dyad Operations Manual
Front View
Control Panel
(Figure 2-1)
(Figure 2-2)
123
456
789
.0-
E N T E R
DYAD
™
P e l t i e r T h e r m a l C y c l e r
D N A E n g i n e
M J R e s e a r c h
Touch pad
Air intake vents
Display screen
Air exhaust vents
Dual-block Alpha
unit, lid closed
P e l t i e r T h e r m a l C y c l e r
D N A E n g i n e
D Y A D
™
Numeric keypad
Touch padKeypad Touch pad “mouse” keysCursor keys
1/4 VGA display screen

2-3
Layout and Specifications
Air intake
vents
Screen contrast adjustment knob External mouse port External mouse/touch pad
selection switch
Back View
Bottom View
(Figure 2-3)
(Figure 2-4) Dyad cycler front
Dyad cycler rear
Alpha unit
handles
Power cord jack Ethernet port
Power switch
RS-232 port
Fuses

2-4
DNA Engine Dyad Operations Manual
Alpha™Units
Single-Block Models
60 Single: Holds 60 x 0.5ml tubes
96 Single: Holds 96 x 0.2ml tubes or
one 96-well microplate
384 Single: Holds one 384-well
microplate
Flat Block: Holds customer-designed
adapter through four screw-
down points
Dual-Block Models
30/30 Dual: Holds 2 x 30 x 0.5ml tubes
30/48 Dual: Holds 1 x 30 x 0.5ml tubes
and 1 x 48 x 0.2ml tubes
48/48 Dual: Holds 2 x 48 x 0.2ml tubes
or half plates
Slide Block
Twin Towers: Holds 2 x 16 standard
slides
Power Bonnet Accessory
Permits remote control of Alpha unit lid opening;
available for Alpha unit models 96, 384, and flat
block.

2-5
Layout and Specifications
Specifications
Thermal range: –5.0°to 105°C, but no more than 30°C below ambient
temperature (4°C to 105°C, but not more than 23°C
below ambient temperature for the Twin Towers®unit)
Accuracy: + 0.3°C of programmed target @ 90°C, NIST-traceable
Thermal uniformity: + 0.4°C well-to-well within 30 seconds of arrival at
90°C (for most Alpha units; see specifications for
individual Alpha units)
Ramping speed: Up to 3°C/sec for all single- and dual-block Alpha units;
Up to 1.2°C/sec for the Twin Towers®unit
Sample capacity: Varies with installed Alpha unit
Line voltage: 200-240VAC
Frequency: 50-60Hz
Power: 1600W maximum
Fuses: Two 6.3A, 250V, 5 x 20mm
Displays: One 1/4 size VGA screen (320x240), 16 colors
Ports: One 9-pin RS-232 serial port
One ethernet port
Memory: 8 MB
Weight: 11kg ( base only)
Size: 48 x 29 x 15cm (l x w x h, base only)
Gradient Specifications (96 Alpha unit 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 seconds
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 for gradient:

2-6
DNA Engine Dyad Operations Manual

Installation
3
Packing Checklist, 3-2
Setting Up the DNA Engine Dyad Cycler, 3-2
Optional External Mouse Device, 3-2
Environmental Requirements, 3-3
Power Supply Requirements, 3-3
Air Supply Requirements, 3-4
Ensuring an Adequate Air Supply, 3-4
Ensuring That Air Is Cool Enough, 3-4
Requirements for Robotics Installations, 3-5
384-Well Microplate Specifics, 3-6

3-2
DNA Engine Dyad Operations Manual
Packing Checklist
After unpacking the DNA Engine Dyad cycler, check to see that you have received the
following:
• One DNA Engine Dyad base
• Two spare fuses
• One power cord
• One external mouse device
•
PTC-220 DNA Engine Dyad Peltier Thermal Cycler Operations Manual
(this
document)
•Product registration card (US & Canada only)
•Extended warranty application (US & Canada only)
If any of these components are missing or damaged, contact MJ Research or the authorized
distributor from whom you purchased the DNA Engine Dyad cycler to obtain a replacement.
Please save the original packing materials in case you need to return the Dyad cycler for
service. See Appendix C for shipping instructions.
Setting Up the DNA Engine Dyad Cycler
The DNA Engine Dyad cycler requires only minimal assembly, plugging in the power cord
and mounting the Alpha units. Insert the power cord plug into its jack at the back of the
machine (see figure 2-3 for location of jack), then plug the cord into a 220V electrical outlet.
With the machine switched off, mount the Alpha units (see the “Installing an Alpha unit”
section in Chapter 4).
Caution: Do not insert or remove an Alpha unit with the Dyad cycler turned on;
electrical arcing can result. Read the safety warning in Appendix A re-
garding electrical safety when inserting or removing an Alpha unit.
Optional External Mouse Device
Included with each shipment of a DNA Engine Dyad™thermal cycler is an externally attach-
able mouse, intended to substitute for the function of the touch pad. Should a Dyad user
prefer an externally attached mouse device, rather than the integrated touch pad, the mouse
should be attached prior to power up of the Dyad cycler.
Underneath the front lip of the Dyad cycler, positioned at the mid-point of the touch pad, are
two connection ports (see figure 2-4). The purple port on the left is reserved for future function
and should not be used. The green port on the right is for connecting the external mouse.
To insure complete compliance with FCC and EMC requirements, only a mouse with a ferrite
core should be used with the Dyad instrument.

3-3
Installation
To connect the mouse, please follow these steps:
1. Verify that the Dyad cycler is off. Wait for 10 seconds to ensure that all fans have
stopped rotating.
2. Grasping the sides of the Dyad cycler, tilt the instrument back so that the underside of the
lip is visible.
3. Line up the pins of the mouse connector with the green port and push the connector into
place.
4. Pull the small switch located behind the purple port into the forward position (see figure
2-4). The rear position will activate only the touch pad. The forward position will activate
only the external mouse device. All Dyad cyclers are shipped with the touch pad enabled
(i.e., the switch is in the rear position). Please note that the cycler will recognize either the
touch pad OR a mouse, but not both input devices simultaneously.
5. Tip the Dyad cycler back down and power up the system.
Environmental Requirements
Ensure that the area where the DNA Engine Dyad cycler is installed meets the following
conditions, for reasons of safety and performance:
•Nonexplosive environment
•Normal air pressure (altitude below 3000m)
•Ambient temperature 5˚–31˚C
•Relative humidity of 10–90% (noncondensing)
•Unobstructed access to air that is 31˚C or cooler (see below)
•Protection from excessive heat and accidental spills. (Do not place the Dyad cycler near
such heat sources as radiators, and protect it from danger of having water or other fluids
splashed on it, which can cause shorting of its electrical circuits.)
Power Supply Requirements
The DNA Engine Dyad cycler requires 200-240VAC, 50-60Hz, and a grounded outlet on a
minimum 20A line. The Dyad cycler can use voltage in the specified range without adjust-
ment, so there is no voltage-setting switch.
Note: Do not cut the supplied power cord and attach a different connector. Use a one-piece
molded connector. If required, additional dedicated power cords may be purchased through
MJ Research or authorized distributors.

3-4
DNA Engine Dyad Operations Manual
Air Supply Requirements
The DNA Engine Dyad cycler requires a constant supply of air that is 31˚C or cooler in order
to remove heat from the Alpha unit’s heat sink. Air is taken in from vents at the bottom and
sides of the machine and exhausted from vents on both sides (see figures 2-1, 2-3, and 2-4).
If the air supply is inadequate or too warm, the machine can overheat, causing performance
problems, software error messages (particularly “HS Overheating”and “Slow Block Cy-
cling”), and even automatic shutdowns. Special attention should be paid to airflow and air
temperature in robotics installations of DNA Engine Dyad cyclers.
Ensuring an Adequate Air Supply
•Do not block the air-intake vents.
Position the DNA Engine Dyad cycler at least 10cm from vertical surfaces and other
thermal cyclers (greater distances may be required; see below). Do not put loose papers,
bench paper, or this manual under the instrument; they can be sucked into the air-intake
vents on the bottom.
•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 com-
pletely clogging up. Check for dust and debris every few months, and clean the intake
vents as needed. Remove light collections of dust with a soft-bristle brush or damp cloth.
Severe collections of dust and debris should be vacuumed out. Turn the instrument off
prior to cleaning or vacuuming air vents.
•Use a solid, non-perforated support material when using the Dyad cycler on a wire rack.
Ensuring That Air Is Cool Enough
•Do not position two or more DNA Engine Dyad cyclers (or other thermal cyclers) so that
the hot exhaust air of one blows directly into the air-intake vents of another.
•Make sure the DNA Engine Dyad cycler receives air that is 31˚C or cooler by measuring
the temperature of air entering the machine through its air-intake vents.
Place the DNA Engine Dyad cycler where you plan to use it, and turn it on. Try to
reproduce what will be typical operating conditions for the machine in that location,
particularly any heat-producing factors (e.g., nearby equipment running, window blinds
open, lights on). Run a typical protocol for 30 minutes to warm up the DNA Engine Dyad
cycler, 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 steps to solve the problem, verify that the temperature of
the air entering the air-intake vents has been lowered, using the procedure outlined
above.

3-5
Installation
Table 3-1 Troubleshooting Air Supply Problems
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erutarepmetriatneibmA .hgihsi tgninoitidnocriatsujdA.erutarepmetriatneibmarewolo
trapmrawnisienihcaM .moorfo taehhcus,morfenihcamtcetorpro,morfyawaenihcamevoM .thgilnusthgirbro,tnempiuqerehto,sretaeh,srotaidarsasecruos
.dedworcerasenihcaM ekatniretnetonseodriatsuahxemrawtahtossenihcamegnarrA .stnev
Requirements for Robotics Installations
Robotics installations require special attention to airflow and air temperature. Typically in
these installations, DNA Engine Dyad cyclers and other thermal cyclers are restricted to a
small area, along with other heat-generating equipment. Overheating can quickly occur
when many of these instruments are operating at once, unless preventive measures are
taken.
Follow the procedures described above to ensure adequate airflow and an air-intake tem-
perature of 31˚C or cooler. Air-intake temperature must be verified by measurement.
Do not use oil or glycerin to thermally couple sample vessels to the blocks of machines in a
robotics installation. This can make plates difficult to remove.

384-Well Microplate Specifics
Some users find that a 384-well microplate can be difficult to remove from the 384-well
block after completing their thermal cycling protocol. The plate fits very snugly in the block,
and the 384 points of contact can provide a significant amount of friction. Fortunately, it is
relatively simple to ameliorate this problem if it occurs in your application.
In our experience, a very thin coating of a Teflon®-based dry lubricant sprayed onto the
block will solve the sticking problem very effectively. The coating eventually wears off so the
block should be re-coated as needed, probably about once every 10 to 20 runs. Your
experience will be the best guide in establishing the frequency for re-coating. As you will
see, a very thin coat is sufficient to eliminate any sticking.
TFE (tetra-fluoroethylene) dry lubricant is available from many sources. One source in the
United States is:
Miller-Stephenson Chemical Co., Inc.
in Danbury, CT: 203-743-4447
in Morton Grove, IL: 847-966-2022
in Sylmar, CA: 818-896-4714
TFE Dry Lubricant/Release Agent
Cat.# MS-122DF (aerosol, 10oz can) approx. $10.50/can
Here are some guidelines for applying the TFE lubricant.
1. Cool the block and lid to room temperature (below 38°C).
2. Cover the lid and any other areas that you don’t want to get slippery.
3. Shake the can well.
4. Spray for about 1 second onto the block.
3-6
DNA Engine Dyad Operations Manual
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