BIO RAD Tetrad 2 User manual

DNA Engine Tetrad®2
Peltier Thermal Cycler
Operations Manual
Version 2.0
PTC-0240 DNA Engine Tetrad 2 Cycler

DNA Engine Tetrad®2
Peltier Thermal Cycler
PTC-0240 DNA Engine Tetrad 2 Cycler
Operations manual
Supports software version 4.0

ii
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, CleanBox, Concord, Disciple Desktop, DNA Engine,
DNA Engine Dyad, DNA Engine Tetrad, Dyad Disciple, Hard-Shell, Hot Bonnet,
iProof, iTaq, Microseal, Moto Alpha, Multiplate, Power Bonnet, Slide Chambers and
Tetrad are trademarks belonging to Bio-Rad Laboratories, Inc.
Teflon is a trademark of E.I. DuPont de Nemours and Company. Windows is a trademark
of Microsoft Corporation.
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 con-
veys 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 corre-
sponding 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.
05184 rev E

iii
Table of Contents
Explanation of Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Safety Warnings and Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Electromagnetic Interference and FCC Warning . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Documentation Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
Chapter 1: Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-1
Chapter 2: Layout and Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-1
Chapter 3: Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-1
Chapter 4: Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-1
Chapter 5: Creating Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-1
Chapter 6: Managing and Editing Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . .6-1
Chapter 7: Running Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-1
Chapter 8: Using the Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-1
Chapter 9: Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-1
Chapter 10: Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-1
Appendix A: Warranties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A-1
Appendix B: End-User and License Agreement . . . . . . . . . . . . . . . . . . . . . . . . . .B-1
Appendix C: Factory-Installed Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C-1
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .In-1
Declaration of Conformity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .DoC-1

iv
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 and Guidelines
Warning: When removing an Alpha unit from a DNA Engine Tetrad 2 base, keep
all fingers and foreign objects away from the Alpha unit bays. Keep all
objects clear of the Alpha unit bays until the fan has come to rest.
Warning: Operating the DNA Engine Tetrad 2 cycler before reading this manual
can constitute a personal injury hazard. Only qualified laboratory per-
sonnel trained in the safe use of electrical equipment should operate
these machines.
Warning: Do not open or attempt to repair the DNA Engine Tetrad 2 cycler, any
Alpha unit, or any accessory to the cycler. Doing so will void your war-
ranties and can put you at risk for electrical shock. Return the
DNA Engine Tetrad 2 cycler to the factory (US customers) or an author-
ized 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 Tetrad 2 cycler incorporates neutral fusing, which
means that live power may still be available inside the machine even
when a fuse has blown or been removed. Never open the
DNA Engine Tetrad 2 base; you could receive a serious electrical shock.
Opening the base will also void your warranty.
Caution: Never remove an Alpha unit from the DNA Engine Tetrad 2 cycler with
the power turned on and a program running. Doing so can cause elec-
trical arcing that can melt the contacts in the connector joining the
Alpha unit to the cycler.
Caution: Do not attempt to unpack or move the DNA Engine Tetrad 2 cycler
alone. Doing so could results in personal injury. Always enlist the help of
another individual when moving or lifting the DNA Engine Tetrad 2 cycler.

Safe Use Guidelines
The DNA Engine Tetrad 2 cycler is designed to be safe to operate under the following
conditions:
• Indoor use
• Altitude up to 2000 m
• Ambient temperature 5–31°C
• Relative humidity 10–90%, 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
Department of Communications.
LE PRESENT APPAREIL NUMERIQUE N'EMET PAS DE BRUITS RADIOELEC-
TRIQUES DEPASSANT LES LIMITES APPLICABLES AUX APPAREILS NUMERIQUES
DE CLASS A PRESCRITES DANS LE REGLEMENT SUR LE BROUILLAGE RADIO-
ELECTRIQUE 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 required to correct the interference at his own expense.
Shielded cables must be used with this unit to ensure compliance with the Class A
FCC limits.
Note Regarding FCC Compliance: Although this design of instrument has been tested and found to comply with Part
15, Subpart B of the FCC Rules for a Class A digital device, please note that this compliance is voluntary, for the
instrument qualifies as an "Exempted device" under 47 CFR § 15.103(c), in regard to the cited FCC regulations in
effect at the time of manufacture.
v

vi
Documentation Conventions
Before describing the various features of the DNA Engine Tetrad 2 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 <PRO-
GRAMS>, <RUN> and <UTILITIES>.
•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
phraseology implying selection of menu or option items with the mouse. In some
instances, selection is also possible by clicking the <<Enter>> button.
___________________________________________________________________________
This instrument system is labeled, “For Research Use Only.”

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

DNA Engine Tetrad 2 Thermal Cycler Operations Manual
1-2 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com
Meet the DNA Engine Tetrad®2 Cycler
Thank you for purchasing an DNA Engine Tetrad 2 cycler. Designed by a team of
molecular biologists and engineers, the DNA Engine Tetrad 2 cycler delivers multi-
block thermal cycling with superior thermal performance. The programmable
DNA Engine Tetrad 2 cycler with its 4-bay chassis is ideal for running multiple proto-
cols and accommodating multiple users.
The DNA Engine Tetrad 2 cycler offers the following features:
• Interchangeable sample blocks—the Alpha™unit family—accommodate a
variety of tubes, microplates, and slides
• Hot Bonnet®heated lid for oil-free cycling or the Moto Alpha™unit for auto-
mated systems
• Intuitive DNA Engine Tetrad 2 system software with user-friendly interface for
programming, editing, file management and much more
• Choice of calculated temperature control for highest speed and accuracy, or
of block or 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 Tetrad 2 cycler
safely and productively:
• Chapter 2 acquaints you with the physical characteristics of the
DNA Engine Tetrad 2 cycler.
• Chapters 3–4 present the basics of installation and operation for the
DNA Engine Tetrad 2 cycler.
• Chapters 5, 6 and 7 describe the creation, editing, and running of programs.
• Chapter 8 outlines the software utilities.
• Chapter 9 explains the proper maintenance of the DNA Engine Tetrad 2
cycler.
• Chapter 10 offers troubleshooting information for the DNA Engine Tetrad 2
cycler.

Introduction
Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 1-3
Important Safety Information
Safe operation of the DNA Engine Tetrad 2 cycler begins with a complete under-
standing of how the instrument works. Please read this entire manual before
attempting to operate the DNA Engine Tetrad cycler. Do not allow anyone who has
not read this manual to operate the instrument.
Warning: The DNA Engine Tetrad 2 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 guidelines at the beginning of
this manual on pages iv and v, and exercise all precautions
outlined in them.
Warning: Do not block the DNA Engine Tetrad 2 cycler’s air vents (see
figs. 2-1 and 2-4 for locations). Obstructing air vents can lead
to overheating and slightly enhanced risk of electrical shock
and fire.

2-1
Layout and
Specifications
2
DNA Engine Tetrad 2 Cycler Front View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-2
DNA Engine Tetrad 2 Cycler Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-2
DNA Engine Tetrad 2 Cycler Back View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-3
DNA Engine Tetrad 2 Cycler Bottom View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-3
Compatible Alpha Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-4
DNA Engine Tetrad 2 Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-5
Gradient Specifications (96-Well Alpha unit only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-5

DNA Engine Tetrad 2 Thermal Cycler Operations Manual
2-2 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com
DNA Engine Tetrad®2 Cycler Front View
(Figure 2-1)
DNA Engine Tetrad 2 Cycler Control Panel
(Figure 2-2)
Numeric keypad
Display screen
Air intake vents
Alpha™unit bay
Keypad
Cursor keys
1/4 VGA display screen
NEXT
BACK
NEXT
BACK

Layout and Specifications
Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 2-3
DNA Engine Tetrad 2 Cycler Back View
(Figure 2-3)
DNA Engine Tetrad 2 Cycler Bottom View
(Figure 2-4)
DNA Engine Tetrad 2 cycler rear
USB A port for mouse
USB B port for
remote command
Air exhaust vent
Air intake vents
Power switch Ethernet port RS-232 port
Fuses Power cord jack

DNA Engine Tetrad 2 Thermal Cycler Operations Manual
2-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com
Compatible Alpha Units
Single-Block Models
60 Single: Holds 60 x 0.5 ml tubes
96 Single: Holds 96 x 0.2 ml 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 0.5 ml tubes
30/48 Dual: Holds 1 x 30 x 0.5 ml tubes
and 1 x 48 x 0.2 ml tubes
48/48 Dual: 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, 384, and flat block formats.

Layout and Specifications
Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 2-5
DNA Engine Tetrad 2 Specifications
Thermal range: 0–105°C, but no more than 30°C below ambient
temperature (10–105°C for the Slide Chambers unit)
Temperature accuracy: +0.3°C of programmed target at 90°C, NIST-traceable
(+0.4°C for dual Alpha units)
Temperature uniformity: +0.4°C well-to-well within 30 seconds of arrival at
90°C (+0.5°C for dual Alpha units)
Speed of ramping: 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: 200–240 VAC
Frequency: 50–60 Hz
Power: 1600 W maximum
Fuses: Two 6.3 A, 250 V, 5 x 20 mm
Displays: One 1/4 size VGA screen (320 x 240), 16 colors
Ports: One 9-pin RS-232 serial port
One ethernet port
Program Capacity: 1,000 (typical)
Weight: 21.6 kg ( base only)
Size: 47 x 61 x 16 cm (l x w x h, base only)
Projected Life Expectancy: 10 years of normal usage (2 protocol runs/day)
7 years of heavy usage (consistently exceeding
2 protocol runs/day)
Gradient Specifications (96-Well Alpha unit only)
Gradient 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
Calculator accuracy: +0.4°C of actual well temperature, NIST-traceable
Lowest temperature 30°C
for gradient:
Highest temperature 105°C
for gradient:
Temperature differential 1–24°C
range:

3-1
Installation
3
Unpacking and Moving the DNA Engine Tetrad 2 Cycler . . . . . . . . . . . . . . . . . . . . . . .3-2
Packing Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-2
Setting Up the DNA Engine Tetrad 2 Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-2
External Mouse Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-5
Requirements for Robotics Installations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-5
384-Well Microplate Specifics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-6

DNA Engine Tetrad 2 Thermal Cycler Operations Manual
3-2 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com
Unpacking and Moving the DNA Engine Tetrad 2 Cycler
Please read the “Unpacking Instructions for the DNA Engine Tetrad®2 Thermal Cycler”
insert in order to properly and safely remove the instrument from its packaging. Always
enlist the help of another individual when moving or lifting the DNA Engine Tetrad 2 cycler.
In order to lift the instrument, grasp the DNA Engine Tetrad 2 cycler from underneath the
chassis (placing your hands on either side of the DNA Engine Tetrad 2 cycler in between
the feet of the instrument) and lift. Do not insert the Alpha™units until the instrument is
located in its final place.
Packing Checklist
After unpacking the DNA Engine Tetrad 2 cycler, check to see that you have received the
following:
• One DNA Engine Tetrad 2 base
• Four spare fuses
• One power cord
• One external mouse device
• DNA Engine Tetrad 2 Peltier Thermal Cycler Operations Manual (this
document)
• Unpacking Instructions for the DNA Engine Tetrad®2 Thermal Cycler
If any of these components are missing or damaged, contact Bio-Rad Laboratories to
obtain a replacement. Please save the original packing materials in case you need to
return the DNA Engine Tetrad 2 cycler for service.
Setting Up the DNA Engine Tetrad 2 Cycler
The DNA Engine Tetrad 2 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 220 V 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 DNA Engine Tetrad 2
cycler turned on; electrical arcing can result. Read the safety warning at the
beginning of this manual on page iv regarding electrical safety when inserting
or removing an Alpha unit.

Installation
Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 3-3
External Mouse Device
Included with each shipment of a DNA Engine Tetrad 2 thermal cycler is an externally
attachable mouse, which should be attached prior to power up of the
DNA Engine Tetrad 2 cycler. Usage of the mouse is required to access full function-
ality of the programming software. Underneath the front lip of the DNA Engine Tetrad
2 cycler are two connection ports (see figure 2-4). The mouse should be connected
to the USB A port.To ensure complete compliance with FCC and EMC requirements,
only a mouse with a ferrite core should be used with the DNA Engine Tetrad 2 instru-
ment.
To connect the mouse, please follow these steps:
1. Verify that the DNA Engine Tetrad 2 cycler is off. Wait for 10 seconds to ensure
that all fans have stopped rotating.
2. Grasping the sides of the DNA Engine Tetrad 2 cycler, tilt the instrument back so
that the underside of the lip is visible.
3. Insert the mouse into the USB A port and push the connector into place.
4. Tip the DNA Engine Tetrad 2 cycler back down and power up the system.
Environmental Requirements
Ensure that the area where the DNA Engine Tetrad 2 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 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
DNA Engine Tetrad 2 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.)