MJ Research PTC-200 DNA Engine User manual

DNA Engine Opticon® System
06678 revC.A
For Continuous Fluorescence Detection
PTC-200 DNA Engine®Cycler
CFD-3200 Opticon™Detector
Operations Manual
Supports Software Version 1.08

DNA Engine Opticon® System
For Continuous Fluorescence Detection
PTC-200 DNA Engine®Cycler
CFD-3200 Opticon™Detector
Operations Manual
Supports Software Version 1.08

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Copyright ©2004, 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.
Chill-out, DNA Engine, DNA Engine Opticon, Hard-Shell, Microseal, MiniCycler, MJ Research and the helix logo,
Multiplate, Opticon, Opticon Monitor and PTC-100 are trademarks belonging to Bio-Rad Laboratories, Inc.
Amplifluor is a trademark of Intergen Company. DyNAzyme is a trademark of Finnzymes Oy. Scorpions is a trade-
mark of DXS Ltd. SYBR is a trademark of Molecular Probes, Inc. TaqMan is a trademark of Roche Molecular Systems,
Inc. Windows is a trademark of Microsoft Corporation.
Practice of the patented polymerase chain reaction (PCR) process requires a license. The DNA Engine Opticon system
includes an Authorized Thermal Cycler and may be used with PCR licenses available from Applied Biosystems. Its use
with Authorized Reagents also provides a limited PCR license in accordance with the label rights accompanying such
reagents .Some applications may also require licenses from other third parties.
This instrument includes an Authorized Thermal Cycler, Serial No __________________. Its purchase price includes the
up-front fee component of a license under United States Patent Nos. 4,683,195, 4,683,202 and 4,965,188, owned by
Roche Molecular Systems, Inc., and under corresponding claims in patents outside the United States, owned by F.
Hoffmann-LaRoche Ltd, covering the Polymerase Chain Reaction ("PCR") process, to practice the PCR process for internal
research and development using this instrument. The running royalty component of that license may be purchased from
Applied Biosystems or obtained by purchasing Authorized Reagents. This instrument is also an Authorized Thermal
Cycler for use with applications licenses available from Applied Biosystems. Its use with Authorized Reagents also
provides a limited PCR license in accordance with the label rights accompanying such reagents. Purchase of this
product does not itself convey to the purchaser a complete license or right to perform the PCR process. Further
information on purchasing licenses to practice the PCR process may be obtained by contacting the Director of Licens-
ing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California, 94404, USA.
No rights are conveyed expressly, by implication or estoppel to any patents on real-time PCR.
Applied Biosystems does not guarantee the performance of this instrument.
06678 revCA

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Table of Contents
Explanation of Symbols .......................................................................................... iv
Safety Warnings .................................................................................................... iv
Safe Use Guidelines................................................................................................. v
Electromagnetic Interference .................................................................................... v
FCC Warning .......................................................................................................... v
1. Introduction ..................................................................................................... 1-1
2. Layout and Specifications ................................................................................. 2-1
3. Installation and Operation ................................................................................ 3-1
4. Compatible Chemistries, Sample Vessels, and Sealing Options ........................... 4-1
5. Introduction to Opticon Monitor™ Software ...................................................... 5-1
6. Experimental Setup and Programming .............................................................. 6-1
7. Run Initiation and Status ................................................................................... 7-1
8. Data Analysis................................................................................................... 8-1
9. Maintenance .................................................................................................... 9-1
10. Troubleshooting ............................................................................................ 10-1
Appendix A .........................................................................................................A-1
Appendix B .......................................................................................................... B-1
Appendix C.......................................................................................................... C-1
Appendix D .........................................................................................................D-1
Appendix E .......................................................................................................... E-1
Index .................................................................................................................. In -1
Declarations of Conformity ............................................................................... DoC -1

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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 com-
ponents 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 per-
sonal injury due to excessive heat if improperly handled.
Safety Warnings
Warning:Warning:
Warning:Warning:
Warning: Operating the DNA Engine Opticon system before reading this manual can
constitute a personal injury hazard. Only qualified laboratory personnel trained
in the safe use of electrical equipment should operate this instrument.
Warning:Warning:
Warning:Warning:
Warning: Do not open or attempt to repair the Opticon tower or base. Doing so will
void your warranties and can put you at risk for electrical shock. Return the
DNA Engine Opticon system to the factory (US customers) or an authorized
distributor (all other customers) if repairs are needed.
Warning:Warning:
Warning:Warning:
Warning: The sample block can become hot enough during the course of normal opera-
tion 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 DNA Engine Opticon system incorporates 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 Opticon base; you could receive a
serious electrical shock. Opening the base will also void your warranties.

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Safe Use Guidelines
The DNA Engine Opticon system is designed to operate safely under the following conditions:
• Indoor use
• Altitude up to 2000m
• Ambient temperature 15˚–25˚C
• Maximum relative humidity 80%, noncondensing
• Transient overvoltage per Installation Category II, IEC 664
• Pollution degree 2, in accordance with IEC 664
Electromagnetic Interference
This device complies with Part 15 of the FCC Rules. Operation is subject to the following
two conditions: (1) this device may not cause harmful interference, and (2) this device
must accept any interference received, including interference that may cause undesired
operation.
This device has been tested and found to comply with the EMC standards for emissions
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
digital apparatus set out in the Radio Interference Regulations of the Canadian Depart-
ment 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 this unit not expressly approved by the party
responsible for compliance could void the user’s authority to operate the equipment.
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 re-
quired to correct the interference at his own expense.

1-1
1. Introduction
Meet the DNA Engine Opticon System, 1-2
Using This Manual, 1-2
Important Safety Information, 1-3

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Opticon System Operations Manual
Meet the DNA Engine Opticon®System
Thank you for purchasing a DNA Engine Opticon continuous fluorescence detection sys-
tem from MJ Research, Incorporated. Designed by a team of molecular biologists and
engineers, the Opticon™system will meet your needs for a sensitive, easy-to-use, and com-
pact continuous fluorescence detection system. Some of the DNA Engine Opticon system’s
many features include:
• A DNA Engine®Peltier thermal cycler delivers superior thermal accuracy and well-to-
well thermal uniformity.
• A 96-well sample block accepts standard consumables (96-well, low-profile micro-
plates and low-profile 0.2ml strip tubes).
• An integrated heated lid permits oil-free cycling.
• Long-lived LEDs excite fluorescent dyes in the 450-495nm range.
• Sensitive optics detect fluorophores with emission spectra in the 515-545nm range
(SYBR Green, FAM).
• Intuitive Opticon Monitor™software facilitates experimental setup, run initiation, run
status, and data analysis.
• Dual modes of temperature control include calculated control for maximum speed
and accuracy, or block control for adapting protocols optimized in other cyclers.
• Compact footprint measuring 47cm deep x 34cm wide x 60cm high, allows the
Opticon unit to fit comfortably on any lab bench.
• The Opticon detector is available separately as an upgrade for existing DNA Engine
thermal cyclers.
Using This Manual
This manual contains instructions for operating your DNA Engine Opticon system safely
and productively:
• Chapter 2 acquaints you with the physical characteristics of the Opticon system.
• Chapter 3 presents the basics of installing and operating the Opticon system.
• Chapter 4 discusses the chemistry and sample vessel compatibilities of the
Opticon system.
• Chapters 5-8 step you through the use of the Opticon Monitor software includ-
ing how to enter and run protocols, and analyze collected data.
• Chapter 9 explains the proper maintenance of the Opticon system.
• Chapter 10 offers troubleshooting information for the Opticon system.

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Introduction
Important Safety Information
Safe operation of the DNA Engine Opticon system begins with a complete understand-
ing of how the instrument works. Please read this entire manual before attempting to op-
erate the DNA Engine Opticon system. Do not allow anyone who has not read this manual
to operate the instrument.
Warning: The DNA Engine Opticon system can generate enough heat to inflict
serious burns and could deliver strong electrical shocks if not used ac-
cording to the instructions in this manual. Please read the safety warnings
and guidelines at the beginning of this manual on pages iv and v, and
exercise all precautions outlined in them.

2-1
2. Layout and Specifications
Front View, 2-2
Back View, 2-2
Specifications, 2-3
Gradient Specifications, 2-4
Computer Specifications, 2-4

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Opticon System Operations Manual
Back View
(Figure 2-2)
Front View
(Figure 2-1)
Power cord jack
(some models)
Power switch
(fuses, some
models)
DAQ (data acquisition)
cable port
Serial cable port
Power module,
left configuration
(standard)
Power cord jack
Power switch
(fuses)
Power module,
right configuration
(some models)
Optical tower
Cycler drawer
Air exhaust vents
(also on other side)
Air intake vents
(also on other side)
Blue protocol-
indicator light
Blue trigger handle
(door mechanism)

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Layout and Specifications
Specifications
Thermal range: 0˚ to 105˚C, but not more than 30˚C
below ambient temperature
Accuracy: ±0.3˚C of programmed target @ 90˚C,
NIST-traceable
Thermal homogeneity: ±0.4˚C well-to-well within 30 seconds of
arrival at 90˚C
Ramping speed: Up to 3.0˚C/sec
Sample capacity: 96-well microplate (low-profile) or
96 x 0.2ml strip tubes (low-profile)
Line voltage: 100-240VAC
Frequency: 50-60Hz
Power: 850W maximum
Fuses: Two 6.3A, 250V Type S505, fast acting
(user changeable)
Two 8.0A, 250V Type S505, fast acting
(inaccessible)
Weight: 27kg (excluding computer and
monitor)
Size: 47cm deep x 34cm wide x 60cm high
(excluding computer and monitor)
Fluorescence Excitation Range: 450-495nm
Fluorescence Detection Range: 515-545nm

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Opticon System Operations Manual
Gradient Specifications
Accuracy: +0.3°C of target at end columns within
30 seconds (NIST-traceable)
Column uniformity: +0.4°C, in column, well–to–well, within
30 seconds of target attainment
Calculator accuracy: +0.4°C of actual column temperature
(NIST-traceable)
Lowest programmable 30°C
temperature:
Highest programmable 105°C
temperature:
Gradient range: from 1°C up to 24°C
(temperature differential)
Computer Specifications
(minimum specifications for the computer provided with the Opticon system)
Processor: 2.4GHz processor
Operating System: Windows XP Pro
Display: 15 inch flat-screen monitor
Memory: 256 MB RAM
Storage: 40GB hard drive
Data Acquisition Board: National Instruments PCI-6036E
200kS/s (samples per second)

3-1
3. Installation and Operation
Unpacking the Opticon Unit, 3-2
Packing Checklist, 3-2
Setting Up the DNA Engine Opticon System, 3-3
Environmental Requirements, 3-3
Power Supply Requirements, 3-4
Air Supply Requirements, 3-4
Ensuring an Adequate Air Supply, 3-4
Ensuring That Air Is Cool Enough, 3-4
Troubleshooting Air Supply Problems, 3-5
Turning the Opticon Unit and Computer On and Off, 3-5
Opening and Closing the Cycler Drawer, 3-6
Loading Sample Vessels into the Block, 3-6

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Opticon System Operations Manual
Unpacking the Opticon™Unit
Please follow these instructions for unpacking the Opticon unit to reduce the risk of per-
sonal injury or damage to the instrument.
Important: DO NOT lift the instrument out through the top of the box.
Important: DO NOT use the blue handle to lift the instrument at any time.
• Cut the band securing the cardboard cover to the support base.
• Open the top of the cardboard cover.
• Remove the top foam insert.
• Remove the accessory box (contents listed below).
• Lift the cardboard cover up and off of the instrument.
• Firmly grasp the sides of the instrument from beneath to support the weight of the
cycler and the optical tower. Carefully lift the instrument off of the shipping sup-
port. Do not lift the instrument by the blue handle or the cycler drawer.
Packing Checklist
After unpacking the DNA Engine Opticon®continuous fluorescence detection system, check
to see that you have received the following:
1. One DNA Engine Opticon unit (Opticon detector with DNA Engine®thermal cycler)
2. One computer with keyboard, mouse, monitor, cables, & installed software (Opticon
Monitor and Windows XP pro)
• One serial cable for connecting the Opticon unit’s serial port (figure 2-2) to the
computer serial port
• One data acquisition cable for connecting the Opticon unit’s DAQ port (figure 2-
2) to the data acquisition card in the computer
3. One Opticon accessory pack including:
• One power cord for the Opticon unit
• Two spare fuses
•
DNA Engine Opticon
®
Continuous Fluorescence Detection System Operations
Manual
(this document)
• Opticon Monitor™software CD ROM
• Consumables samples including 0.2ml low-profile strip tubes in opaque white
(MJ Research catalog no. TLS-0851), optical flat caps for 0.2ml tubes and plates
(MJ Research catalog no. TCS-0803), and low-profile Multiplate™96-well micro-
plates in opaque white (MJ Research catalog no. MLL-9651)

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Installation and Operation
If any of these components are missing or damaged, contact MJ Research, Incorporated or
the authorized distributor from whom you purchased the DNA Engine Opticon system to
obtain a replacement. Please save the original packing materials in case you need to return
the DNA Engine Opticon system for service. See Appendix C for shipping instructions.
Setting Up the DNA Engine Opticon System
The Opticon system requires a location with three power outlets to accommodate the
Opticon unit, the computer, and the monitor. A location with network access (Ethernet
10/100BaseT) is recommended if you wish to transfer setup and analysis files between
the computer running the Opticon unit and other computers.
The DNA Engine Opticon system requires only minimal assembly. Insert the power cord
plug into its jack at the back of the instrument, just below the power switch (see figure 2-
2 for the location of the jack). Then, plug the power cord into a standard 110V or 220V
electrical outlet. The Opticon unit will accept 220V automatically, as does the monitor.
However, you must set the voltage on the computer. See the “Power Supply Requirements”
section below for more information.
Before launching the Opticon Monitor software (see Chapter 5), be sure that the Opticon
unit is connected to the computer. There are two cables that connect the Opticon unit to
the computer. Connect the serial cable to the serial cable port on the Opticon unit (see
figure 2-2) and serial port #2 on the computer. Connect the data acquisition cable to the
DAQ port on the Opticon unit (see figure 2-2) and the data port on the computer.
Note: The DAQ cable has high-density connectors; take care not to bend any of the pins.
Environmental Requirements
For reasons of safety and performance, ensure that the area where the DNA Engine
Opticon system is installed meets the following conditions:
• Nonexplosive environment
• Normal air pressure (altitude below 2000m)
• Ambient temperature 15˚–31˚C
• Relative humidity above 10% and up to 80%
• 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
Opticon system near such heat sources as radiators, and protect it from danger of
having water or other fluids splashed on it, which can cause electrical short circuits.)

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Opticon System Operations Manual
Power Supply Requirements
The DNA Engine Opticon unit requires 100-240VAC, 50-60Hz and a grounded outlet.
The DNA Engine Opticon unit can use current in the specified range without adjustment,
so there is no voltage-setting switch. The monitor can also accept either 110 or 220V
power without adjustment.
Important! For 220V operation of the computer, the red voltage-setting
switch located on the back of the computer, near the power cord
jack, must display 230V rather than 115V.
The Opticon unit is equipped with a power-entry module that accepts cordsets with an
IEC 60320-1 type C13 connector (this is the same standard configuration used by many
computer manufacturers for their equipment). All cordsets used with the Opticon unit must
be rated to carry at least 10A at 125V or 250V, the latter specification depending upon
the supply voltage used. Additionally, the cordset must meet all other applicable national
standards—thus at a minimum, the cordset should carry the mark of a nationally recog-
nized testing agency appropriate to your nation.
Note: Do not cut the supplied 120V power cord and attach a different connector. Use a one-
piece molded connector of the type specified above.
Air Supply Requirements
The DNA Engine Opticon unit requires a constant supply of air that is 31˚C or cooler in
order to remove heat from the heat sink. Air is taken in from the lower vents located on
the sides of the instrument and exhausted from the upper vents on both sides (see figure
2-1). If the air supply is inadequate or too hot, the instrument can overheat, causing per-
formance problems and even automatic shutdowns.
Ensuring an Adequate Air Supply
• Do not block air intake vents (see figure 2-1).
Position the DNA Engine Opticon unit at least10cm from vertical surfaces and other thermal
cyclers or heat-generating equipment (greater distances may be required; see below).
• Do not allow dust or debris to collect in the air intake vents.
Ensuring That Air Is Cool Enough
• Do not position two or more DNA Engine Opticon units (or other instruments) so that hot
exhaust air blows directly into the air intake vents.
• Confirm that the DNA Engine Opticon unit receives air that is 31˚C or cooler by measur-
ing the temperature of air entering the machine through its air intake vents.