Bio-Rad PTC-1148 Operation Manual
MJ Mini™Gradient Thermal Cycler
Operations Manual
PTC-1148 MJ Mini Thermal Cycler
i
MJ Mini™Gradient Thermal Cycler
Operations Manual
PTC-1148 MJ Mini Thermal Cycler
MJ Mini Gradient Thermal Cycler Operations Manual
ii
Copyright ©2005, Bio-Rad Laboratories, Incorporated. Reproduction in any form, either print or electronic, is prohibited without written permission of Bio-Rad Laboratories, Inc.
Chill-Out, Hot Bonnet, Microseal, MiniCycler, MJ Mini, MJ Research, Mini Opticon and the helix logo
are trademarks belonging to Bio-Rad Laboratories, Inc.
NOTICE TO PURCHASER
Purchase of this instrument, Serial No. ____________, 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 MJ Mini thermal cycler, when combined with a MiniOpticon 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.
10968 rev D
iii
Table of Contents
Explanation of Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Safety Warnings and Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .iv
Electromagnetic Interference and FCC Warning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v
Documentation Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi
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. Using the Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-1
9. Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-1
10. Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-1
Appendix A: Warranties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A-1
Appendix B: Factory-Installed Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-1
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .In-1
Declaration of Conformity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .DoC-1
MJ Mini Gradient Thermal Cycler Operations Manual
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
Warning: Operating the MJ Mini Peltier thermal 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 this machine.
Warning: Do not open or attempt to repair the MJ Mini cycler base, the power
supply, the heat pump/sample block, or other accessory. Doing so will void your warranties and can put you at risk for electrical shock. Return the MJ Mini cycler to the
factory (US customers) or an authorized distributor (all other customers) if repairs are
needed.
Warning: The sample 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 MJ Mini cycler 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 cycler base; you could receive a serious electrical
shock. Opening the base will also void your warranties.
Safe Use Guidelines
The MJ Mini is designed to be safe to operate under the following conditions:
• Indoor use
• Altitude up to 2000 m
• Temperature 5˚C to 40˚C
• Maximum relative humidity 80% for temperatures up to 31˚C, decreasing
linearly to 50% relative humidity at 40˚C
• Mains supply voltage fluctuations not to exceed ±10% of the nominal voltage
• Installation Categories (Overvoltage categories) II
• Pollution degree 2
• Electrical Supply, 100-240 VAC, 50-60 Hz, 400 W
v
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 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 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.
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.
MJ Mini Gradient Thermal Cycler Operations Manual
vi
Documentation Conventions
Documentation Conventions
Typographic Conventions
The names of keyboard keys are encased 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 can display up to seven
lines of text at one time.
Example
Terminology
A programming option is termed “selected” when the option is highlighted. In this
manual, the selected terms are outlined (see the example above).
New: Lid:100˚C
ABCD Vol: 20µL
1= 92.0˚ FOR 0:30
2=
LOWER TEMP ˚C:
1-1
Introduction
1
Meet the MJ Mini Thermal Cyclers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
Using This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
Important Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-3
MJ Mini Gradient Thermal Cycler Operations Manual
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Meet the MJ Mini Thermal Cyclers
Thank you for purchasing an PTC-1148 MJ Mini thermal cycler. This personal sized
cycler features:
• Premium cycling in a medium capacity cycler: the MJ Mini can hold 48 x 0.2 ml
tubes, 12 x 0.5 ml tubes or one 48-well microplate.
• Ability to program and maintain a 16˚C temperature gradient, front-to-back,
along the block for protocol optimization in a single run.
• Upgradability to a real-time PCR system with the addition of the Mini Opticon™
real-time detector.
• Integrated Hot Bonnet® heated lid for oil-free thermal cycling. The heated lid
pressure may be manually adjusted to permit the seating of different vessels.
• Intuitive software with an easy-to-read interface for rapid input of programs,
which may contain advanced protocol steps such as auto-time extension, auto-temperature increment, and variable ramp rates.
• 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.
• Customizable factory-installed protocols.
Using This Manual
This manual contains all the information you need to operate your MJ Mini thermal
cycler safely and productively:
• Chapter 2 acquaints you with the physical characteristics of this cycler.
• Chapters 3–5 present the basics of installing and operating the MJ Mini cycler.
• Chapters 6 and 7 describe programming.
• Chapter 8 outlines the utilities available on the MJ Mini cycler.
• Chapter 9 explains the proper maintenance, and Chapter 10 offers trou-
bleshooting information for this system.
Introduction
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Important Safety Information
Safe operation of the MJ Mini begins with a complete understanding of how the
machine works. Please read this entire manual before attempting to operate the
system. Do not allow anyone who has not read this manual to operate this machine.
Warning: The MJ Mini 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 precautions outlined in them.
Warning: Do not block the MJ Mini cycler’s air vents (see figs. in Chapter 2 for
locations). Obstructing air vents can lead to overheating and slightly enhanced risk
of electrical shock and fire.
2-1
Layout and
Specifications
2
Front View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-2
Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-2
Back View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-3
Bottom View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-3
Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-3
Gradient Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-4
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Front View
Figure 2.1
Control Panel
Figure 2.2
Heated lid closed
Thumbwheel
Control panel
Screen hot key
LCD window
Proceed key
Selection keys
Cancel key
Block heating/
cooling lights
Pause key
Layout and Specifications
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Back View
Figure 2.3
Bottom View
Figure 2.3
Heated lid
Power switch
Fuses
Air intake vents
Air exhaust vents
Front
Back
Jack for power cord
USB ports
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Specifications
Thermal range: 0–99.9˚C, but no more than 30˚C below ambient
temperature
Thermal accuracy: ±0.2˚C of programmed target @ 90˚C, NIST-traceable
Thermal uniformity: ±0.4˚C well-to-well within 10 sec of arrival at 90˚C
Ramping speed: Average ramp rates are 1.5˚C/sec, with a maximum
rate of 2.5˚C/sec
Sample capacity: 48 x 0.2 ml tubes, 12 x 0.5 ml tubes, or one 48-well
microplate
Line voltage: 100–240 VAC rms (no adjustment needed among
voltages within these ranges)
Frequency: 50–60 Hz single phase
Power: 400 W maximum
Fuses: Two 6.3 A, 250 V, 5 x 20 mm
Displays: 64 x 128 backlit LCD
Ports: Two USB ports allowing retrofitting to MiniOpticon
real-time PCR system, daisy-chaining of MJ Mini
cyclers, and communications or remote control with
an external PC.
Memory: 400 typical programs in 12 folders
Weight: 4.1 kg
Size (W x D x H): 18 x 32 x 20 cm
Gradient Specifications
Temp gradient accuracy:
±
0.2°C of programmed target at end rows, 10 sec after
the timer starts for the gradient step, NIST–traceable
Thermal row uniformity: ±0.4°C , in row, well-to-well, within 10 sec of reaching
target temperature
Calculator accuracy: ±0.4°C of actual row temperature, NIST-traceable
Lowest programmable temperature: 35°C
Highest programmable temperature: 99°C
Temperature differential range: 1–16°C
3-1
Installation
3
Packing Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-2
Setting Up the MJ Mini Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .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
MJ Mini Gradient Thermal Cycler Operations Manual
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Packing Checklist
After unpacking the MJ Mini thermal cycler, check to see that you have received the
following:
• One MJ Mini thermal cycler
• Two spare fuses
• One power cord
• MJ Mini Gradient Thermal Cycler Operations Manual (this document)
If any of these components is missing or damaged, contact Bio-Rad Laboratories to
obtain a replacement. Please save the original packing materials in case you need to
return the instrument for service. See Appendix C for shipping instructions.
Setting Up the MJ Mini Instrument
The MJ Mini cycler requires minimal assembly: plugging in the power cord. 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.
Environmental Requirements
Ensure that the area where the thermal 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 80%
• Unobstructed access to air that is 31˚C or cooler (see below)
• Protection from excessive heat and accidental spills. (Do not place the MJ Mini
near such heat sources as radiators, and protect it from the danger of having water
or other fluids splashed on it, which can cause shorting in its electrical circuits.)
Installation
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Power Supply Requirements
The MJ Mini thermal cycler requires 90–240 V, 50–60 Hz, and a grounded outlet. This
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 120 V 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 MJ Mini thermal cycler requires a constant supply of air. Air is taken in from vents
at the front of the instrument is exhausted from vents at the back (see fig. 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.
Ensuring an Adequate Air Supply
• Do not block the air intake vents.
Position the MJ Mini at least 10 cm from vertical surfaces and other thermal cyclers
(greater distances may be required; see below). Do not put loose papers under or in
front of the machine; they can be sucked into the air vents and cause problems.
• Do not allow dust or debris to collect in the air intake vents.
The 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.
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Ensuring That Air Is Cool Enough
• Do not position two or more thermal cyclers so that the hot exhaust air of one
blows directly into the air intake vents of another.
• Make sure the MJ Mini receives air that is 31˚C or cooler by measuring the temperature of air entering the machine through its air intake vents. Air intake vents are
located at the front of the machine (see fig. 2-4).
Place the thermal 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 (e.g., BASIC) for 30 minutes to warm up the cycler,
then measure the air temperature at the 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.
Cause Possible Remedies
Air circulation is poor. Provide more space around machine or adjust room ventilation.
Ambient air temperature Adjust air conditioning to lower ambient air temperature.
is high.
Machine is in warm part Move machine away from, or protect machine from, such heat
of room. sources as radiators, heaters, other equipment, or bright sunlight.
Machines are crowded. Arrange machines so that warm exhaust air does not enter intake
vents.
4-1
Operation
4
Turning the MJ Mini Cycler 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-4
Opening and Closing a Sample Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-4
Selecting the Correct Sample Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-4
0.5 ml Tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-4
Thin-Walled Vs. Thick-Walled Tubes . . . . . . . . . . . . . . . . . . . . . . . . . .4-5
0.2 ml Tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-5
Microplates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-5
Sealing Sample Vessels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-5
Sealing with Oil or Wax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-5
Sealing with the Hot Bonnet Lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-6
Adjusting the Hot Bonnet Lid’s Pressure . . . . . . . . . . . . . . . . . . . . . . .4-7
Loading Sample Vessels into the Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-8
Using Oil to Thermally Couple Sample Vessels to the Block . . . . . . . . . . . . .4-8
Appendix 4-A Tube, Microplate, and Sealing System Selection Chart . . . . . . . .4-9
Appendix 4-B Safety Warning Regarding Use of
35
S Nucleotides . . . . . . . . . . .4-10
The Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-10
96-well Polycarbonate Microplates . . . . . . . . . . . . . . . . . . . . . . . . . .4-10
0.2 ml Polypropylene Tubes and Polypropylene Microplates . . . . . .4-10
0.5 ml Polypropylene Tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-10
The Solution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-11
MJ Mini Gradient Thermal Cycler Operations Manual
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Turning the MJ Mini Cycler On
Move the power switch to “o” (the “On” position). The fan will turn on, and the
Cooling/Heating lights on the keyboard will flash. The MJ Mini will enter a self-test
of the heat pumps.
Note: If the sample block or the heat sink is not at ambient temperature (typically
because the sample block was recently in use), the machine will skip the self-test.
If the self-test does not detect any problems, the Main Menu is displayed.
Alternatively, depressing the «Screen» button will bring you to the main screen.
The MJ Mini is now ready to execute programs.
Understanding the Main Menu
The Main Menu is the common access point to all programming and machine configuration screens:
• RUN: Executes a program.
• NEW: Allows new programs to be entered.
• EDIT: Allows modification of stored programs.
• VIEW: Accesses utilities that display a program’s steps.
• FILES: Accesses file management utilities.
• TOOLS: Accesses machine configuration screens.
RUN VIEW
NEW FILES
EDIT TOOLS
Block is idle
Operation
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Using the Control Panel
The control panel (see fig. 2-2) includes operation keys, status indicator lights for
heating and cooling, an LCD window for displaying programming and machine
status text, and a numeric keypad for entering values into programs.
Operation Keys
• Select keys (left, right, up, down arrows): Move the cursor one space or option
in the LCD window.
• Proceed/Enter: Accepts a selected menu or screen option; during a protocol run,
advances the program to its next step.
• Cancel: Terminates a running protocol; during program creation or editing, can-
cels the last entry.
• Pause: Pauses a protocol during execution.
• Instant: Initiates a program that sets up the MJ Mini as a simple incubator.
• Screen: Switches between protocol status screens, the Main Menu and a time
remaining display in the LCD window during a protocol run. In addition, this button
toggles between the Main Menu and the “About” screen for the instrument, and
allows the users to alternately view the text and graphical programming screens.
Status Indicator Lights
• Block Status lights: Indicate whether the sample block is heating (red light is illu-
minated) or cooling (blue light is illuminated).
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Using the Data Ports
The MJ Mini thermal cycler has two USB ports located at the rear of the machine, a
USB A (upper) port and a USB B (lower) port. These ports allow the MJ Mini thermal
cycler to be connected in series and operated centrally from a single PC. The USB A
port is used to connect the first cycler to the PC and the USB B port connects to the
USB A port or the next MJ Mini cycler in the chain. Up to four instruments may be
serially connected in this manner. Alternatively, up to four MJ Mini thermal cyclers
may be connected to a PC via a USB hub.
Protocols are programmed and run from the PC using Opticon Monitor
™
software
(which is available for download from our website). Note that a separate instance of
the software should be opened for each networked MJ Mini cycler.
Opening and Closing a Sample Block
Grip the front handle of the Hot Bonnet®heated lid and pull upward firmly. The top
lever will pop open to reveal the entire thumbwheel. Continue pulling upward to open
the Hot Bonnet. The Hot Bonnet will tip backward, revealing the entire block.
Caution: Do not pull on the thumbwheel to open the unit. This can damage the Hot
Bonnet’s closing mechanism.
To close the sample block, 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.
Selecting the Correct Sample Vessel
The MJ Mini accepts both 0.2 ml and 0.5 ml tubes as well as 48-well microplates.
Keep in mind that differences in tube and plate composition and wall thickness
among the many brands available can affect reaction performance. Protocols may
require some adjustment to ensure optimum performance when using a new vessel
type. Bio-Rad offers a full range of tubes and microplates manufactured to the specifications of sample block of MJ line cyclers. See chapter appendix 4-A for a
complete list.
0.5 ml Tubes
It is possible to load up to twelve 0.5 ml tubes in the MJ Mini cycler. Since the width
of the 0.5 ml tubes does not allow them to be accommodated in adjacent wells, the
tubes should be placed in a staggered fashion (i.e., in every other well in the block).
The tubes should NOT be placed in the spaces between wells. Furthermore,
placement of tubes in the peripheral wells along the edge of the cycler block should
be avoided, as this may result in compromised amplification due to condensate formation. For correct placement of 0.5 ml tubes, see Figure 4-1.
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When using 0.5 ml tubes, thin-walled tubes are recommended; these are specifically
designed for thermal cycling and the higher-quality brands provide a good and consistent fit. If thick-walled 0.5 ml tubes are used, ensure that they fit the wells snugly.
(Since these tubes were originally designed for centrifuges, some brands may not fit
tightly in thermal cycler wells.) Both thin and thick-walled 0.5 ml tubes are available
from Bio-Rad and are designed for precise block fit.
Thin-Walled Vs. Thick-Walled Tubes
The thickness of sample tubes directly affects the speed of sample heating and thus
the amount of time required for incubations. Thick-walled tubes delay sample
heating, since heat transfers more slowly through the tubes’ walls. For the earliest
types of thermal cyclers this delay mattered little. These machines’ ramping rates
were so slow (below 1°C/sec) that there was plenty of time for heat to transfer
through the tube wall to the sample, during a given incubation.
Modern thermal cyclers have much faster ramping rates, so the faster heat transfer
provided by thin-walled tubes allows protocols to be significantly shortened.
Essentially, up to 30 seconds can be saved per cycle by using thin-walled tubes, for
an overall savings of 15 minutes in a 30-cycle run.
0.2 ml Tubes
All types of thin-walled 0.2 ml tubes may be used. Bio-Rad sells high-quality 0.2 ml
tubes in a number of styles, including individual tubes and strips.
Microplates
A variety of polypropylene 48-well microplates can be used in the MJ Mini cycler as
long as they fit the wells snugly. In addition, the Multiplate line of 96-well plates and
Microseal
®
film seals can be cut down to fit in the sample block of this instrument.
Polypropylene microplates and compatible Microseal film or strip caps for sealing
Figure 4-1. Wells () in which 0.5 ml tubes should be placed
Operation
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are available from Bio-Rad Laboratories.
Sealing Sample Vessels
To avoid changing the concentration of reactants, steps must be taken to prevent the
evaporation of water from reaction mixtures during thermal cycling. Only a layer of
oil or wax will completely prevent evaporation from the surface of the reaction fluid.
However, an adequate degree of protection can be achieved by sealing vessels with
caps, film, or adhesive seals then cycling the samples using the heated lid to prevent
condensation.
Sealing with Oil or Wax
Mineral oil, silicone oil, paraffin wax, or Chill-out™ liquid wax may be used to seal
samples. Use only a small amount of oil or wax; 1-3 drops (15–50 µl) are usually sufficient. (Include this volume in the total volume when setting up a calculated-control
protocol; see “Choosing a Temperature Control Mode” in chapter 5.) Use the same
amount of oil or wax in all sample vessels to ensure a uniform thermal profile.
Most paraffin waxes solidify at room temperature. The wax can then be pierced with
a micropipette tip and the samples drawn off from below the wax. Silicone oil and
mineral oil can be poured off or aspirated from tubes if the samples are first frozen
(–15° to –20°C). The samples are usually pure enough for analysis without an extraction.
Chill-out liquid wax (available from Bio-Rad Laboratories) is an easy-to-use alternative to oil. This purified paraffinic oil solidifies at 10°C and is liquid at room
temperature. By programming a holdstep at low temperature, the wax can be solidified at the end of a run. A pipette tip can then be used to pierce the wax in the tubes
and remove the samples. The wax is available in a clear, optical-assay grade or dyed
red to assist in monitoring its use. The red dye has no adverse effects on fluorescent
gel analysis of reaction products.
Sealing with the Hot Bonnet Lid
The Hot Bonnet’s heated inner lid maintains the air in the upper part of sample vessels at a higher temperature than the reaction mixture. This prevents condensation
of evaporated water vapor onto the vessel walls and lid, so that solution concentrations are unchanged by thermal cycling. The Hot Bonnet lid also exerts pressure on
the tops of vessels loaded into the block, helping to maintain a vapor-tight seal and
to firmly seat tubes or the plate in the block.
Caps, film, adhesive seals, or mats must be used along with the Hot Bonnet lid to
prevent evaporative losses.
Note: When tubes are cooled to below-ambient temperatures, a ring of condensa-
Operation
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tion may form in tubes above the liquid level but below the top of the sample block.
This is not a cause for concern since it occurs only at the final cool-down step, when
thermal cycling is complete.
Microseal® 'A' film offers a quick alternative to sealing microplates or arrays of tube
strips. This film is specially designed to seal tightly during cycling, yet release
smoothly to minimize the risk of aerosol formation and cross-contamination of samples. Microseal 'A' film, designed to cover a 96-well plate, is easily cut for use with
fewer than 96 samples.
Microseal 'B' adhesive seals feature an aggressive adhesive, effective from –20°C to
110°C, which allows secure sample storage or transport before and after cycling.
The clear polyester backing allows easy inspection of sample wells. Microseal 'B'
clear, adhesive seals are ideal for thermal cycling in all polypropylene and polystyrene microplates. Microseal 'B' adhesive seals can be easily cut for use with fewer
than 96 samples.
Microseal 'F' aluminized foil acts as a barrier against evaporation from –20˚C to
105˚C. In addition to cold storage applications, it can also be used for thermal
cycling sample volumes ≥25 µl. The foil is thin enough to pierce with a pipet tip for
recovery of sample from individual wells. Microseal 'F' foil is easily cut for use with
fewer than 96 samples.
Adjusting the Hot Bonnet Lid’s Pressure
The pressure exerted by the Hot Bonnet lid must be manually adjusted to fit the
sample vessels being used. Once set, the Hot Bonnet lid can be opened and closed
repeatedly without readjustment as long as neither the tube or microplate type nor
the sealing method is changed. Any change in vessel type or sealing method
requires readjustment of the Hot Bonnet lid.
Follow these steps to adjust the pressure exerted by the inner lid:
1. Make sure the block’s wells are clean. Even tiny amounts of extraneous material
can decrease thermal conductance and interfere with the proper seating of a
microplate or tubes.
2. Open the Hot Bonnet lid. Turn the thumbwheel all the way counterclockwise to
completely raise the inner lid.
3. Load either a microplate or at least eight individual tubes into the sample block.
The inner lid pivots around a central point, so it is important to distribute individual
tubes evenly: load at least four tubes in the center of the block and at least one tube
in each of the four corners of the block. If using a sealing film or mat, apply it to the
loaded microplate according to the manufacturer’s directions.
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4. Close the Hot Bonnet lid by pressing down on the top lever. Turn the thumbwheel
clockwise to lower the inner lid onto the loaded microplate/tubes. The thumbwheel
turns easily at first since the inner lid has not yet come into contact with anything.
Stop turning the thumbwheel when you feel increased resistance, which indicates
that the inner lid has touched the microplate/tubes.
5. For microplate sealing films or mats that require additional pressure, turn the
thumbwheel clockwise an extra half turn past the point of initial contact to set an
appropriate lid pressure.
Caution: Do not turn the thumbwheel more than three-quarters of a turn. This can
make it hard or impossible to close the lid and puts excessive strain on the latch
holding the lid closed.
An extra half to three-quarters of a turn ensures the correct pressure for most types
of reaction vessels. Some empirical testing may be required to determine the
optimum pressure required for certain vessels. Once this pressure has been determined, the thumbwheel position may be marked with a colored marking pen or piece
of tape.
Note: As an aid in gauging how much the thumbwheel has been turned, mark it at
the quarter turn positions, or every sixth “bump” on the thumbwheel (there are 24
total “bumps”).
Loading Sample Vessels into the Block
When using a small number of tubes, load at least one empty tube in each corner of
the block to ensure that the Hot Bonnet lid exerts even pressure on the sample tubes
(see “Adjusting the Hot Bonnet Lid’s Pressure,” above).
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:
• Ensure that the block is clean before loading samples (see chapter 9 for cleaning
instructions).
• Firmly press individual tubes or the microplate into the block wells.
Using Oil to Thermally Couple Sample Vessels to the Block
With two exceptions (see below), Bio-Rad does not recommend using oil to thermally couple sample vessels to the block, for the following reasons:
• Calculated-control protocols do not run accurately when oil is used.
• Oil traps dirt, which interferes with thermal contact between vessels and the
block.
Operation
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• Calculated-control protocols do not run accurately when oil is used.
• Oil traps dirt, which interferes with thermal contact between vessels and the block.
Caution: If you use oil in the block, use only mineral oil. Never use silicone oil. It can
damage the sample block.
One exception to this recommendation involves the use of volatile radioactive 35S
nucleotides. A small amount of oil in the block can help prevent escape of these compounds. See appendix 4-B of this chapter for important information regarding safe use
of these compounds in polypropylene tubes and polypropylene and polycarbonate
microplates. A second exception involves the use of thick-wall 0.5 ml tubes. Certain
brands of these tubes fit poorly in the block, in which case, oil may somewhat improve
thermal contact. Whenever possible, use high-quality thin-wall tubes intended for
thermal cycling (see appendix 4-A of this chapter for a tube and plate selection chart).
Appendix 4-A Tube, Microplate, and Sealing System
Selection Chart
The following sample vessels and sealing options are recommended for use with the MJ
Mini thermal cycler. These items are available from Bio-Rad Laboratories.
Key
Reaction vessel fits block/sealing option fits reaction vessel without modification.
Reaction vessel/sealing option can be cut to fit.
Thermal
Cycler
Sealing Options for Oil-Free CyclingReaction Vessels
MJ Mini
Bio-Rad
catalog #
Microseal
‘A’ film
MSA-5001
Microseal
‘B’ seal
MSB-1001
Microseal
‘F’ foil
MSF-1001
Strip caps
TCS-series
Chill-out
wax
CHO-series
Description
MLP-series
MLL-series
Multiplate unskirted
96-well microplates
MLP-series
Multiplate unskirted
48-well microplates
MLP-2401
Multiplate unskirted
24-well microplates
TBS-series
TLS-series
0.2 ml strip tubes
8/strip & 12/strip
TFI-0201
TBI-series
0.2 ml individual tubes
TBI-series
0.5 ml individual tubes,
w/ caps
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Appendix 4-B Safety Warning Regarding Use of 35S
Nucleotides
Some researchers have experienced a problem with radioactive contamination when
using 35S in thermal cyclers. This problem has occurred with all types of reaction
vessels.
The Problem
When 35S nucleotides are thermally cycled, a volatile chemical breakdown product
forms, probably SO
2
. This product can escape the vessel and contaminate the
sample block of a thermal cycler, and possibly, the air in the laboratory.
Contamination has been reported with microassay plates, 0.2 ml tubes, and 0.5 ml
tubes.
0.2 ml Polypropylene Tubes and Polypropylene Microplates
These tubes are manufactured with very thin walls to enhance thermal transfer. The
thin walls are somewhat fragile and can “craze” or develop small cracks when subject to mechanical stress. Undamaged thin polypropylene tubes may also be
somewhat permeable to the
35
S breakdown product. Either way, there have been
reports of
35
S passing through the walls of 0.2 ml tubes of several different brands
during thermal cycling. No data are yet available on radioactive contamination with
polypropylene microplates.
0.5 ml Polypropylene Tubes
Contamination problems are rarer with this type of tube, but instances have been
reported.
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