BIO RAD PTC-200 User manual

DNA Engine®Thermal Cycler
Operations Manual
Version 4.0
PTC-200 DNA Engine Cycler

DNA Engine®Peltier Thermal
Cycler
PTC-0200 DNA Engine Cycler
Operations Manual
Version 4.0

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Copyright ©2005, Bio-Rad Laboratories, Incorporated. All rights reserved. Reproduction in any form, either print or electronic,
is prohibited without written permission of Bio-Rad Laboratories, Inc.
Alpha, Chill-out, Concord, Dual Alpha, DNA Engine, DNA Engine Tetrad, Hard-Shell, Hot Bonnet, Microseal, Moto Alpha,
Multiplate, Power Bonnet, Remote Alpha Dock, Slide Chambers, and Tetrad are trademarks of Bio-Rad Laboratories, Inc.
NOTICE TO PURCHASER
This base unit, Serial No. ____________, in combination with its immediately attached Bio-Rad sample block module(s),
constitutes a thermal cycler whose purchase conveys a limited non-transferable immunity from suit for the purchaser’s own
internal research and development and for use in applied fields other than Human In Vitro Diagnostics under one or more of U.S.
Patents Nos. 5,656,493, 5,333,675, 5,475,610 (claims 1, 44, 158, 160-163 and 167 only), and 6,703,236 (claims 1-7 only), or
corresponding claims in their non-U.S. counterparts, owned by Applera Corporation. No right is conveyed expressly, by
implication or by estoppel under any other patent claim, such as claims to apparatus, reagents, kits, or methods such as 5’
nuclease methods. Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Applied
Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
This DNA Engine thermal cycler, when combined with a Chromo4 detection module bearing a valid label license under U.S.
Patent No. 6,814,934, constitutes a real-time thermal cycler licensed under U.S. Patent No. 6,814,934 and corresponding claims
in any Canadian counterpart patent thereof owned by Applera Corporation, for use solely in research and all applied fields
except human and veterinary in vitro diagnostics, provided that the real-time thermal cycler royalty fee that is applicable to said
thermal cycler has been paid. No rights are conveyed expressly, by implication or estoppel to any patents on real-time methods,
including but not limited to 5' nuclease assays, or to any patent claiming a reagent or kit. For further information on purchasing
license rights, contact the Director of Licensing at Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California, 94404,
USA.
05434 rev E

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Explanation of Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Safety Warnings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Safe Use Guidelines, Electromagnetic Interference, and FCC Warning . . . . . . . . . . . . .v
Documentation Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
The DNA Engine®Peltier Thermal Cycler
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-1
Layout and Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-1
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-1
Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-1
Running Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-1
Creating Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6-1
Editing Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-1
Using the Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-1
Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-1
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-1
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11-1
The Remote Alpha Dock™System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12-1
Appendix A: Warranties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A-1
Appendix B: Factory-Installed Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-1
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .In-1
Declaration of Conformity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .DoC-1
Table of Contents

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Explanation of Symbols
CAUTION: Risk of Danger! Wherever this symbol appears, always consult
note in this manual for further information before proceeding. This symbol
identifies components that pose a risk of personal injury or damage to the
instrument if improperly handled.
CAUTION: Risk of Electrical Shock! This symbol identifies components that
pose a risk of electrical shock if improperly handled.
CAUTION: Hot Surface! This symbol identifies components that pose a risk
of personal injury due to excessive heat if improperly handled.
Safety Warnings
Warning: Operating the DNA Engine®cycler before reading this manual can
constitute a personal injury hazard. Only qualified laboratory personnel
trained in the safe use of electrical equipment should operate these
machines.
Warning: Do not open or attempt to repair the DNA Engine or any Alpha™
unit, or other DNA Engine accessory. Doing so will void your warranties and
can put you at risk for electrical shock. Return the DNA Engine instrument to
the factory (US customers) or an authorized distributor (all other customers) if
repairs are needed.
Warning: All Alpha unit blocks can become hot enough during the course of
normal operation to cause burns or cause liquids to boil explosively. Wear
safety goggles or other eye protection at all times during operation.
Warning: The DNA Engine instruments incorporate neutral fusing, which
means that live power may still be available inside the machines even when a
fuse has blown or been removed. Never open the DNA Engine or DNA Engine
Tetrad base; you could receive a serious electrical shock. Opening the base
will also void your warranties.
Caution: Never remove an Alpha unit from the DNA Engine with the power
turned on and a program running. Doing so can cause electrical arcing that
can melt the contacts in the connector joining the Alpha unit to the DNA
Engine.

Safe Use Guidelines
The DNA Engine instruments are designed to be safe to operate under the following
conditions:
• Indoor use
• Altitude up to 2000 m
• 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
These devices comply with Part 15 of the FCC Rules. Operation is subject to the following
two conditions: (1) these devices may not cause harmful interference, and (2) these devices
must accept any interference received, including interference that may cause undesired
operation.
These devices have been tested and found to comply with the EMC standards for emis-
sions and susceptibility established by the European Union at time of manufacture.
This digital apparatus does not exceed the Class A limits for radio noise emissions from dig-
ital apparatus set out in the Radio Interference Regulations of the Canadian Department of
Communications.
LE PRESENT APPAREIL NUMERIQUE N’EMET PAS DE BRUITS RADIOELECTRIQUES
DEPASSANT LES LIMITES APPLICABLES AUX APPAREILS NUMERIQUES DE CLASS A
PRESCRITES DANS LE REGLEMENT SUR LE BROUILLAGE RADIOELECTRIQUE
EDICTE PAR LE MINISTERE DES COMMUNICATIONS DU CANADA.
FCC Warning
Warning: Changes or modifications to these units not expressly approved by the party
responsible for compliance could void the user’s authority to operate the equipment.
This equipment qualifies as an “Exempted device” under Section 15.103(c) of the FCC Rules.
Nonetheless, the design has been verified to comply within limits for Class “A” digital device.
Note: This equipment has been tested and found to comply with the limits for a Class A
digital device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide
reasonable protection against harmful interference when the equipment is operated in a
commercial environment. This equipment generates, uses, 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 this equipment in a residential
area is likely to cause harmful interference in which case the user will be required to correct
the interference at his own expense.
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Documentation Conventions
Typographic Conventions
The names of keyboard keys are set in double angle brackets:
Example «Proceed»
Items in programming menus are italicized:
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
Terminology
A programming 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 displayed in all-capital letters.
Run: 2-STEP
1= 92.0 for 0:05
Cycle: 1
Calc: 65.0

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

DNA Engine Operations Manual
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Meet the DNA Engine®Thermal Cycler
Thank you for purchasing a Bio-Rad PTC-0200 DNA Engine thermal cycler. Designed
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.
• Interchangeable sample blocks—the Alpha™unit family— that accommodate
many types of tubes, microplates, and slides
• Hot Bonnet®heated lid (or its remote-controlled version, the motorized Moto
Alpha™Moto Alpha unit) for oil-free cycling
• Intuitive software with easy-to-read interface for quick and painless programming,
editing, file management, password protection, and much more
• Choice of calculated sample temperature control for highest speed and accuracy, or
block control for compatibility with protocols designed for a variety of instrument types
• Space-saving design for easy setup and transportation
• Instant Incubate feature for continuous-temperature incubations
• Networking of up to 15 machines, for convenient remote operation and documentation
of runs
• Customizable factory-installed protocols
Using This Manual
This manual contains all the information you need to operate your DNA Engine safely
and productively:
• Chapter 2 acquaints you with the physical characteristics of the DNA Engine.
• Chapters 3–5 present the basics of installing and operating the DNA Engine.
• Chapters 6 and 7 describe programming the DNA Engine.
• Chapter 8 outlines the utilities available for the DNA Engine.
• Chapter 9 describes how to network and remotely operate the DNA Engine.
• Chapter 10 explains the proper maintenance of the DNA Engine.
• Chapter 11 offers troubleshooting information for the DNA Engine.

Introduction
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Important Safety Information
Safe operation of the DNA Engine begins with a complete understanding of how the
machine works. Please read this entire manual before attempting to operate the DNA
Engine. Do not allow anyone who has not read this manual to operate the machine.
The DNA Engine 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 guidelines at the front of this manual, and exercise all pre-
cautions outlined in them.

2-1
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
Moto Alpha Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-4
Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-5
Gradient Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-6

Front View
(Figure 2-1)
Control Panel
(Figure 2-2)
DNA Engine Operations Manual
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Alpha™unit, lid closed Thumbwheel
Air intake vents
Control panel
Air exhaust vents
(also on other side)
Block status lights
Instant incubation key
Power light
Block key
LCD window
Left and right
selection keys
Proceed key
Cancel key

Layout and Specifications
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Back View
(Figure 2-3)
Bottom View
(Figure 2-4)
Air exhaust vents
(also on other side)
Alpha unit
Air intake vents
Alpha unit handle
Power cord jack
RS-232 port IEEE-488 port
Parallel printer port
Back Front
Air intake vents

Alpha Units
Single-Block Models
60V Alpha unit: Holds 60 x 0.5 ml tubes
96V Alpha unit: Holds 96 x 0.2 ml tubes or
one 96-well microplate
384 Alpha unit: Holds one 384-well
microplate or one 96-well
microplate
Dual-Block Models
30/30 Dual Alpha™Holds 2 x 30 x 0.5
unit: ml tubes
30/48 Dual Alpha unit: Holds 1 x 30 x 0.5 ml
tubes and 1 x 48 x
0.2 ml tubes
48/48 Dual Alpha unit: Holds 2 x 48 x 0.2 ml
tubes or half plates
Slide Block
Slide Chambers™Alpha unit: Holds 2 x 16
standard slides
Moto Alpha™unit
Permits remote control of Alpha unit lid opening;
available in 96-well, 384-well, and flat-block
formats.
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Layout and Specifications
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Specifications
Thermal range: –5° to 105°C, but no more than 30°C below ambient
temperature (4° to 100°C for the Slide Chambers Alpha unit)
Thermal accuracy: ±0.3°C of programmed target at 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 Slide Chambers Alpha unit.
Sample capacity: Varies with installed Alpha unit
Line voltage: DNA Engine®cycler: 100–240 VAC rms (no adjustment
needed among voltages within these ranges)
Frequency: 50–60 Hz single phase
Power: DNA Engine cycler: 850 W maximum
Fuses: Two 6.3 A, 250 V, 5 x 20 mm
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 purpose interface bus
Memory: 400 typical programs in up to 12 individual folders

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Gradient Specifications (96V Alpha module only)
Accuracy: +0.3°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
Gradient calculator accuracy: +0.4°C of actual well temperature
Lowest programmable temp: 30°C
Highest programmable temp: 105°C

3-1
Installation
3
Packing Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-2
Setting Up the DNA Engine Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-4

DNA Engine Operations Manual
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Packing Checklist
After unpacking the DNA Engine®cycler, check to see that you have received the fol-
lowing:
• One DNA Engine base
• One Alpha™unit (more if additional units were ordered)
• Two spare fuses
• One power cord
• DNA Engine Peltier Thermal Cycler, Operations Manual (this document)
If any of these components are missing or damaged, contact Bio-Rad or the authorized dis-
tributor from whom you purchased the DNA Engine cycler to obtain a replacement. Please
save the original packing materials in case you need to return the DNA Engine cycler for
service. See appendix A for warranty information.
Setting Up the DNA Engine Cycler
The DNA Engine cycler 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, insert an Alpha unit (see “Installing an Alpha Unit,” chapter 4).
Caution: Do not insert or remove an Alpha unit with the DNA Engine cycler
turned on; electrical arcing can result. Read the safety warning at
the front of this manual regarding electrical safety when inserting or
removing an Alpha unit.
Environmental Requirements
Ensure that the area where the DNA Engine cycler is installed meets the following
conditions, for reasons of safety and performance:
• Nonexplosive environment
• Normal air pressure (altitude below 2000 m)
• Ambient temperature 5–31°C
• Relative humidity up to 90%
• Unobstructed access to air that is 31°C or cooler (see below)

Installation
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• Protection from excessive heat and accidental spills (Do not place the DNA Engine
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 in its electrical cir-
cuits.)
Power Supply Requirements
The DNA Engine cycler requires 100–240 VAC, 50–60 Hz, and a grounded outlet. The DNA
Engine cycler can use current in the specified range without adjustment, so there is no
voltage-setting switch.
Power cords for outlets other than the US 120V outlet may be purchased from computer
stores, since they are also used for most desktop computers and printers and meet
international standard IEC-320. The power cord must be rated to carry at least 10 A at
125 V or 250 V, depending on the voltage available in your nation. The quality of the
power cord can be further ensured by making certain it is inscribed with the trademark
of UL, CSA, TUV, VDE, or another national testing agency.
Note: Do not cut the supplied 120 V power cord and attach a different connector.
Use a one-piece molded connector of the type specified above.
Air Supply Requirements
The DNA Engine 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 front,
back, and bottom of the machine and exhausted from vents on both sides (see figs. 2-
1, 2-3, and 2-4). If the air supply is inadequate or too hot, the machine can overheat,
causing performance problems, software error messages (particularly “HS Overheating”
and “Slow Block Cycling”), and even automatic shutdowns. Special attention should be
paid to airflow and air temperature in robotics installations of DNA Engine cyclers.
Ensuring an Adequate Air Supply
• Do not block the air intake vents.
Position the DNA Engine cycler at least 10 cm from vertical surfaces and other thermal
cyclers (greater distances may be required; see below). Do not put loose papers under
the machine; they can be sucked into the air intake vents on the bottom of the machine.
• 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. 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 machine
off prior to cleaning or vacuuming air vents.