Manual Del Termociclador MJ-PTC-100-PCR-1

PTC-100 Operations Manual
Version 8.1
MJ Research™, Incorporated
Boston • San Francisco • Tahoe • Copenhagen • Seoul
Copyright ©1997, MJ Research™, Incorporated. All rights reserved.
PTC-100, PTC-100HB, 16MS Slide Block, Chill-out, Frame-Seal, Hot Bonnet, Microseal, Self-Seal,
Slide Griddle, MJ Research marks and helix logo are trade and/or service marks belonging to MJ
Research, Incorporated.
06107-AA
Thermal cyclers can be used for a number of purposes, including the polymerase chain reaction
(PCR). PCR is covered by patents owned by Hoffmann-La Roche, Inc., and F. Hoffmann-La Roche,
Ltd., who have granted exclusive and nonexclusive licenses for some types of applications. Roche
and its licensees provide end-user licenses within their respective fields. These licenses have dif-
ferent terms depending on the particular application of PCR, and different rules may apply in
different countries. Anyone who intends to use MJ RESEARCH equipment to do PCR is encouraged
to contact Hoffmann-La Roche for more information, at one of the addresses below:
In the United States: In other nations:

Licensing Manager PCR Licensing Manager
Roche Molecular Systems, Inc. F. Hoffmann-La Roche Ltd.
1145 Atlantic Avenue Building 222/350
Alameda, CA 94501 USA CH-4002 Basel, Switzerland
(510) 814-2970 41-61-687-3031
Fax: (510) 814-2977 Fax: 41-61-687-2113
ii
Contents
Documentation Conventions ............................................................................................... iv
1. Introduction ................................................................................................................. 1-1

2. Layout and Specifications .......................................................................................... 2-1
3. Installation .................................................................................................................... 3-1
4. Operation ...................................................................................................................... 4-1
5. Running Protocols ....................................................................................................... 5-1
6. Programming ............................................................................................................... 6-1
7. Editing Programs ........................................................................................................ 7-1
8. Maintenance ................................................................................................................. 8-1
9. Troubleshooting ........................................................................................................... 9-1
Appendix A: The 16MS Slide Block ................................................................................ A-1

Appendix B: Safety Warnings .......................................................................................... B-1
Appendix C: Factory-installed Protocols ....................................................................... C-1
Appendix D: Warranties ................................................................................................... D-1
Appendix E: Shipping Instructions for US Residents .................................................. E-1
Index ..................................................................................................................................... In-1
Declaration of Conformity ............................................................................................... DoC-1
iii
Documentation Conventions
Typographic Conventions
The names of keyboard keys are in sans serif type and placed within
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 two lines of text:
Example: RUN Enter

Program Program
Terminology
A programming option is termed “selected” when the cursor is positioned
in front of it. Use the «Select» keys (see fig. 2-3) to move the cursor. In
some screens selected items are also displayed in all-capital letters.
iv
1 Introduction
Meet the PTC-100 ......................................... 1-2
How to Use This Manual .............................. 1-2
Important Safety Information ..................... 1-2
1-1
Meet the PTC-100

Thank you for purchasing an MJ RESEARCH PTC-100 thermal cycler. De-
signed by a team of molecular biologists and engineers, the PTC-100 will
meet your needs for an easy-to-use, reliable, compact programmable ther-
mal cycler:
• Easy-to-read programming interface for quick and painless program-
ming, editing, file management, and much more
• Choice of block or probe control
• Space-saving design for easy setup and transportation
• Instant Incubate feature for continuous-temperature incubations
• Hot Bonnet heated lid for oil-free cycling
• Customizable factory-installed protocols
How to Use This Manual

This manual contains all the information you need to operate the PTC-100
safely and productively:
• Chapter 2 describes the physical characteristics and specifications
of the PTC-100.
• Chapters 3–5 describe installing and operating the PTC-100.
• Chapters 6 and 7 describe programming the PTC-100.
• Chapter 8 describes proper maintenance of the PTC-100.
• Chapter 9 offers advice on troubleshooting the PTC-100.
Note: Information on installing, operating, and programming the 16MS

Slide Block cycler may be found in appendix A.
Important Safety Information

Safe operation of the PTC-100 begins with a complete understanding of
how the machine works. Please review this entire manual before attempt-
ing to operate the PTC-100. Do not allow anyone who has not reviewed
this manual to operate the machine.
The PTC-100 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 in appen-
dix B, and exercise all precautions outlined in them.
1-2
2 Layout and Specifications
PTC-100 with Cold Lid .................................. 2-2

Models Available ..................................................... 2-2
Front View (Figure 2-1) ............................................. 2-2
Back View (Fig. 2-2) ................................................. 2-3
Control Panel (Fig. 2-3) ............................................ 2-3
PTC-100 with Hot Bonnet ............................. 2-4

Models Available ..................................................... 2-4
Front View (Fig. 2-4) ................................................. 2-4
Back View (Fig. 2-5) ................................................. 2-5
PTC-100 with 16MS Slide Block (Fig. 2-6) ...... 2-6
Accessories ................................................. 2-7

Temperature Probe (Fig. 2-7) .................................... 2-7
Slide Griddle Adapter (Fig. 2-8) ............................... 2-7
Specifications .............................................. 2-8
2-1
PTC-100 with Cold Lid
Models Available
60-well block: holds 60 x 0.5ml tubes
96-well block: holds 96 x 0.2ml tubes or one 96-well microplate
96AgV gold/silver block: holds 96 x 0.2ml tubes or one 96-well microplate; block is gold-
plated sterling silver for faster ramping speed
16MS Slide Block: holds sixteen 25 x 75mm slides and 24 x 0.2ml tubes (see p. 2-6)
Front View (Fig. 2-1)
Lid
Control panel
Air exhaust vents
Air intake vents
2-2
Layout and Specifications
Back View (Fig. 2-2)
Probe jack
On-off switch
Chart recorder jack

Power cord jack
Hot Bonnet jack (unused

in this model)
Parallel printer port
Air intake vents
Control Panel (Fig. 2-3)
LCD window
Cancel key
1 2 3
4 5 6 Left and right
selection keys
7 8 9
0 Proceed key
LED bar graph
2-3
PTC-100 with Hot Bonnet
Models Available
60-well block: holds 60 x 0.5ml or 0.6ml microcentrifuge tubes
96-well block: holds 96 x 0.2ml tubes or one 96-well microplate
96AgV gold/silver block: holds one 96-well microplate or 96 x 0.2ml tubes; block is gold-
plated sterling silver for faster ramping speed
Front View (Fig. 2-4)
Thumbwheel
Lid release button

Hot Bonnet
Control panel
Air exhaust vents
Air intake vents
2-4
Back View (Fig. 2-5)
On-off switch
Chart recorder jack

Power cord jack
Hot Bonnet jack (with

cord plugged in)
Parallel printer port
Hot Bonnet cord
Air intake vents
2-5
PTC-100 with 16MS Slide Block

(Fig. 2-6)
Slide block
Plastic pin
Control panel
Air exhaust vents
Air intake vents
2-6
Accessories
Temperature Probe (Fig. 2-7)
Allows machine to control reactions according to a representative sample’s temperature. Avail-
able for the 60-well model of the PTC-100, with or without the Hot Bonnet.
Probe jack
Probe tube, with sensor inside
Slide Griddle Adapter (Fig. 2-8)

Allows machine to thermally cycle up to four 25 x 75mm glass slides. Two models are available:
the actively controlled adapter and the passive adapter. Available for 60-well and 96-well models
of the PTC-100, with or without the Hot Bonnet.
Active slide griddle Passive slide griddle
2-7
Specifications
Thermal range: 0–100°C
Accuracy: ±0.5°C of programmed target at 60°C
Thermal homogeneity: ±0.4°C well to well within 30 seconds of arrival at 60°C
16MS slide block: ±0.4°C within 30 seconds of arrival at 90°C
Ramping rate: 60-well block: up to 1°C/sec
96-well: up to 1.2°C/sec
96AgV gold/silver block: up to 2.5°C/sec
16MS Slide Block: up to 0.5°C/sec
Sample capacity: 60-well block: Sixty x 0.5ml tubes
96-well block, 96AgV gold/silver block: 96 x 0.2ml tubes or
one 96-well plate
16MS Slide Block: Sixteen 25 x 75mm slides and 24 x 0.2ml
tubes
Line voltage: 100–240VAC rms (no adjustment needed among voltages
within these ranges)
Frequency: 50/60Hz single phase
Power: 350W maximum (momentary 4.5 A)
Fuses: Two 4A, 5 x 20mm (4 ampere)
Displays: One 2 x 16 LCD alphanumeric display
Ports: One 25-pin 8-bit parallel interface printer port
Memory: 360 typical programs, in nonvolatile memory; programs may
contain up to 100 steps; maximum of 1600 steps among all
programs
Weight: 7.0kg
Size: PTC-100 with cold lid, 24cm x 28cm x 23cm; PTC-100 with
Hot Bonnet, 23cm x 28cm x 26cm
2-8
3 Installation
Packing List ................................................. 3-2
Setting Up the PTC-100 ................................ 3-2
Environmental Requirements ....................... 3-2
Power Supply Requirements ....................... 3-3
Air Supply Requirements ............................. 3-3
3-1
Packing List
After unpacking the PTC-100, make sure you have received the following:
• One PTC-100, with Hot Bonnet if ordered
• One power cord
• Two fuses
• One sponge rubber pad (with 96-well block, for cold lid machines
only)
• The PTC-100 Operations Manual (this document)
If any of these components are missing or damaged, contact MJ RESEARCH
or the authorized distributor from whom you purchased the PTC-100 to
obtain a replacement. Please save the original packing materials in case
you need to return the PTC-100 for service. See appendix E for shipping
instructions.
Setting Up the PTC-100

Insert the power cord plug into its three-pronged jack at the back of the
machine (see fig. 2-2), then plug the cord into an electrical outlet (see
“Power Supply Requirements,” below).
For the PTC-100 with Hot Bonnet, screw the Hot Bonnet power cord into its
jack at the back of the machine (see fig. 2-5; finger-tightness is adequate).
Situate the machine according to the instructions below.
Environmental Requirements
Ensure that the area where the PTC-100 is installed meets the following
conditions, for reasons of safety and performance:
• Indoor use, nonexplosive environment
• Normal air pressure (altitude below 2000m)
• Ambient temperature 4–32°C
• Humidity10–90%
• Protection from excessive heat (e.g., radiators) and accidental spills
3-2
Installation
Power Supply Requirements

The PTC-100 requires 100–240VAC, 50–60Hz, 850W, and a grounded out-
let. The machine can use current in the specified range without adjust-
ment, so there is no voltage-setting switch.
Air Supply Requirements

Air is taken in from vents at the rear and sides and on the bottom of the
machine and exhausted from vents at both sides of the machine. If the ma-
chine does not get enough air or gets air that is too warm, it can overheat.
Overheating can cause the machine to display a warning message, “H[eat]
S[ink] Overheating, Check Air Flow,” or even to shut itself off.
To prevent overheating, position the machine at least 10cm from other
thermal cyclers or walls. If the ambient air temperature exceeds 32°C,
use fans or adjust the air conditioning to cool the air that the machine
receives. Keep the air intake vents clean and free of obstructions such as
loose sheets of paper.
3-3
4 Operation
Turning the PTC-100 On ............................... 4-2 Using the Probe .......................................... 4-10
Customizing the Probe Vessel ................................... 4-10
Using the Control Panel ............................... 4-2 Adding the Oil .......................................................... 4-11
Operation Keys ........................................................ 4-2 Loading and Connecting the Probe .......................... 4-12
Status Indicator Lights ............................................... 4-3 Running a Protocol under Probe Control .................. 4-12
Calibrating the Probe ............................................... 4-12
Opening and Closing the Lid ........................ 4-3

Appendix 4-A: Tube, Microplate, and Sealing
System Selection Chart ................................ 4-14
Selecting the Correct Sample Vessel ............ 4-3
0.5ml Tubes .............................................................. 4-3
0.2ml Tubes .............................................................. 4-3 Appendix 4-B: Safety Warning Regarding
Microplates .............................................................. 4-4 Use of 35S Nucleotides ................................. 4-15
Thin-Walled Vs. Thick-Walled Tubes .......................... 4-5
Sealing Sample Vessels ............................... 4-5

Sealing with Oil or Wax ........................................... 4-5
Sealing with the Hot Bonnet and Caps or Film .......... 4-6
Adjusting the Hot Bonnet’s Lid Pressure ............. 4-7
Loading Sample Vessels .............................. 4-8

Using the Sponge Rubber Pad with the 96V Block ... 4-9
Using Oil to Improve Thermal Contact ...................... 4-9
Using the Slide Griddle ................................ 4-10
4-1
Turning the PTC-100 On

Move the power switch at the right rear of the machine to “1” (the “On”
position). In most cases, a self-test of the heat pump will begin running
(see note below). Its progress is tracked in a screen in the LCD window:
SELF TEST
*
This screen disappears within 10 seconds. If a problem is detected, an

error message is displayed.
Note: If either the heat sink or the block is not between 17 and 30°C, the
machine will skip the self-test.
Following the self-test, the Run-Enter Menu is displayed:
_RUN Enter
Program Program
The PTC-100 is now ready to execute programs.
Using the Control Panel

The control panel (see fig. 2-3) includes operation keys, status indicator
lights, an LCD window for displaying programming and machine status
text, and a numeric keypad for entering values into programs.
Operation Keys
• Select keys (left and right arrows): Move the cursor one space or op-
tion to the left or right in the LCD window.
• Proceed: Accepts a selected menu or screen option.
• Cancel: Terminates a running protocol; during program creation or
editing, cancels the last entry.
• Stop: Terminates a running protocol.
• Pause: Pauses a protocol during execution; accesses Japanese Katakana
syllabary.
• Instant Incubate: Initiates a program that sets up the PTC-100 as a
simple incubator.
4-2
Operation
Status Indicator Lights

• Power light: Glows red when the PTC-100 is powered up.
• LED bar graph: Glows red along its top half when the machine is heat-
ing; glows green along its bottom half when the machine is cooling.
Opening and Closing the Lid

Opening the 60-block PTC-100 with cold lid: Lift the lid (there is no
latch) (fig. 4-1A, p. 4-4).
Opening all other PTC-100s with cold lids: Gently push on the
metal latch at the front of the lid (fig. 4-1B) until it disengages,
then lift the lid.
Opening the PTC-100 with Hot Bonnet: Push on the blue button at the
lid’s center front and lift the lid (fig. 4-1C).
Closing all PTC-100 models: Push the lid down to cover the block. Make
sure that lid pressure is correctly adjusted on Hot Bonnet models.
Selecting the Correct Sample Vessel

MJ RESEARCH offers a full range of tubes and microplates, manufac-
tured to the specifications of each type of block to ensure a precise fit.
See chapter appendix 4-A for a complete list. Keep in mind that dif-
ferences 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 us-
ing a new vessel type.
0.5ml Tubes
Make sure thick-walled 0.5ml tubes fit the wells snugly. Since these tubes
were originally designed for centrifuges, some brands may not fit tightly
in thermal cycler wells. Thin-walled 0.5ml tubes were specifically de-
signed for thermal cycling, and the higher quality brands provide a good
and consistent fit. MJ RESEARCH provides thin- and thick-walled 0.5ml tubes
designed for precise block fit.
0.2ml Tubes
All types of thin-walled 0.2ml tubes may be used. MJ RESEARCH sells
high-quality 0.2ml tubes in a number of styles, including individual
tubes and strips.
4-3
Microplates
A variety of 96-well polypropylene or polycarbonate microplates may be
used in 96-well blocks as long as they fit the wells snugly. Polypropylene
microplates are usually preferred because they exhibit very low protein
binding and, unlike polycarbonate microplates, do not lose water vapor
through the vessel walls. This allows smaller sample volumes to be used—
as little as 5–10µl. Polypropylene microplates and compatible Microseal
‘A’ film, mats, or strip caps for sealing are available from MJ RESEARCH.
(See “Sealing with the Hot Bonnet and Caps or Film,” p. 4-6, for a de-
scription of Microseal ‘A’.)
Figure 4-1 A, Opening the 60-well block PTC-100 with cold lid. B, Opening all other PTC-100s with
cold lids. C, Opening the PTC-100 with Hot Bonnet.
A B
4-4
Operation
Thin-Walled Vs. Thick-Walled Tubes

The thickness of sample tubes directly affects the speed of sample heat-
ing and thus the amount of time required for incubations. Thicker 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.
Many modern thermal cyclers have much faster ramping rates (up to 2–
3°C/second), so the faster heat transfer provided by thin-walled tubes
allows protocols to be significantly shortened. For example, in the reac-
tion illustrated in figure 4-2 (p. 4-6), over 30 seconds can be saved per
cycle by using thin-walled tubes, for an overall savings of 15 minutes in
a 30-cycle run.
Sealing Sample Vessels

Steps must be taken to prevent the evaporation of water from reaction
mixtures during thermal cycling, to avoid changing the concentration of
reactants. Only a layer of oil or wax will completely prevent evaporation
from sample vessels, and this sealing method must be used when cycling
samples in PTC-100s that do not have the Hot Bonnet. However, an ad-
equate degree of protection can be achieved by sealing with Microseal
film, mats, or caps, then cycling the samples using the Hot Bonnet heated
lid to prevent condensation/refluxing. (See appendix A for information
on sealing slides for use in the 16MS Slide Block.)
Sealing with Oil or Wax

Mineral oil, silicone oil, paraffin wax, or Chill-out liquid wax may
be used to seal sample vessels. Use only a small amount of oil or
wax; 1–3 drops (15-50µl) are usually sufficient. Use the same amount
of oil or wax in all sample vessels to ensure a uniform thermal profile.
Some paraffin waxes solidify at room temperature. The wax can then be
pierced with a micropipette and the samples drawn off. 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 analy-
sis without an extraction.
4-5
Chill-out liquid wax (available from MJ RESEARCH) is an easy-to-use alter-

native to oil. This purified paraffinic oil solidifies at 14°C and is liquid at
room temperature. By programming a hold step at low temperature, the
wax can be solidified at the end of a run. A pipette can then be used to
pierce the wax in the tubes and remove the samples. The wax is dyed red
to assist in monitoring its use. The dye has no known adverse effects on
fluorescent gel analysis of reaction products.
Sealing with the Hot Bonnet and Caps or Film

The Hot Bonnet heated lid (available for all PTC-100 blocks except the
96U block and the 16MS Slide Block) maintains the air in the upper part
of sample vessels at a higher temperature than the reaction mixture. This
prevents condensation, refluxing, and changes in reactant concentrations.
The Hot Bonnet 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.
Figure 4-2 Ramping rate enhancement with thin-walled tubes. To compare ramping rates of sample tem-
perature, 50µl samples of water were cycled in 0.5ml thin- and thick-walled tubes in a PTC-
200 thermal cycler with a 60-well block. Thermal profile: 94°C, 120 sec; 62°C, 120 sec. Data
are shown for the third cycle. The cycler was run under block control, and the Hot Bonnet was
heated to 105°C and tightened to a half-turn past the touch point. The samples in thin-walled
tubes reached the target temperature more quickly.
{
17-sec
difference
Block
Thin wall
Thick wall
{
15-sec difference
4-6
Operation
Caps, film, or mats must be used along with the Hot Bonnet to prevent
evaporative losses. Tight-fitting caps do the best job of preventing vapor
loss (and should be used for long-term storage of reaction products).
Microseal ‘A’ film is a quick way to seal Multiplate and “Concord”
microplates or large arrays of tubes. This film is specially designed to
seal tightly during cycling yet release smoothly, which minimizes the risk
of aerosol formation and cross-contamination of samples. Microseal ‘A’
is easily cut for use with fewer than 96 wells.
Microseal ‘M’ rubber sealing mats are an economical means to seal 96-
well microplates. An array of 96 dimples on the mat helps orient it on the
microplate and prevents the mat from sticking to the Hot Bonnet’s heated
lid. The mats may be cleaned with sodium hypochlorite for reuse and are
autoclavable.
Note: After a hold at below-ambient temperatures, a ring of condensa-

tion may form in tubes or microplate wells above the liquid level but
below the top of the block. This is not a cause for concern since it occurs
only at the final cool-down step, when thermal cycling is finished.
Adjusting the Hot Bonnet’s Lid Pressure

The pressure exerted by the inner lid of the Hot Bonnet must be manu-
ally adjusted to fit a given type of tube or microplate, sealed in a given
way. Once set, the Hot Bonnet can be opened and closed repeatedly with-
out readjustment, as long as neither the tube or microplate type nor the
sealing method changes. Any change in vessel type or sealing method
requires readjustment of the Hot Bonnet’s lid.
Follow these steps to adjust the pressure exerted by the Hot Bonnet’s
inner lid:
1. Make sure the block’s wells are clean. Even tiny amounts of extraneous
material can interfere with the proper seating of tubes or a microplate,
which would prevent the lid from exerting uniform pressure on the
loaded tubes or microplate.
2. Open the Hot Bonnet. Turn the blue thumbwheel all the way coun-
terclockwise to completely raise the inner lid.
3. Load either a microplate or at least eight individual tubes into the
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 according to the
manufacturer’s directions.
4-7
4. Close the Hot Bonnet. Turn the thumbwheel clockwise to lower the
Hot Bonnet’s inner lid onto the loaded tubes/microplate. 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 tubes/microplate.
5. Open the Hot Bonnet. Turn the thumbwheel clockwise an extra half
to three-quarters of a turn to set an appropriate lid pressure.
Note: 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 for certain vessels. Once this pres-
sure has been determined, the thumbwheel position that delivers it may
be marked with a colored marking pen or piece of tape.
✔ Tip: 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”).
6. Close the Hot Bonnet. You will hear a click when the lid latch en-
gages. If the latch does not engage, the lid is not closed. Firm pressure
may be required to engage the latch.
Loading Sample Vessels

When using a small number of tubes, they should all be placed in the
center of the block, to ensure uniform thermal cycling of all samples. If
using the Hot Bonnet, also load at least one empty tube in each corner of
the block, to ensure that the Hot Bonnet exerts even pressure on the tubes
(see “Adjusting the Hot Bonnet’s Lid Pressure,” p. 4-7).
To obtain 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:
• Check that the block is clean before loading samples (see chapter 8
for cleaning instructions).
4-8
Operation
• Firmly press the tubes or microplate into the block wells.
Note: See appendix A for information on loading slides into the 16MS
Slide Block.
Using the Sponge Rubber Pad with the 96-well Block

In PTC-100 models with the 96-well block and the cold lid, a sponge rub-
ber pad may be used to help seat tubes or a plate into the block. Attach
the magnetic backing of the pad to the inner surface of the lid. When the
lid is closed, the pad will press loaded tubes or plate down into the wells.
Caution: Never use the sponge rubber pad with the Hot Bonnet
heated lid. The pad will block transmission of heat to the
tops of loaded vessels, causing reaction failures. The
heated lid is able to firmly seat vessels into the block, with-
out the assistance of the pad.
Using Oil to Improve Thermal Contact

A small amount of oil may be placed within block wells to improve heat
transfer from the block to loaded vessels and to help prevent the escape
of radioactive 35S nucleotides when using polypropylene tubes and
polypropylene or polycarbonate microplates (see chapter appendix 4-B).
Using oil requires care, attention, and cooperation on the part of every-
one who uses the machine, in order to avoid the problems associated
with its use:
• It can be messy.
• If used in excess of recommended amounts, it can seep into the ma-
chine and damage internal components.
• It must be used consistently. If a protocol is designed to be run with
oil in the block, oil must always be used for the protocol in order to
ensure replicable results.
The first time you put oil into the block, put two drops into each well that
will be holding a sample vessel. Thereafter, more oil must generally be
added every two to three times the machine is used.
Each time you run a protocol requiring oil, make sure sufficient oil is
present in the wells:
• When using tubes: Insert a tube, remove it, and visually inspect for
the presence of oil on the outside of the tube. If none is visible, add a
drop of oil to the well. Repeat for each tube loaded.
4-9
• When using a plate: Follow the same procedure as for tubes. If no oil
is visible on the outside of the plate, add a drop of oil to each well in
the block.
Excess oil in any well will overflow onto the top surface of the block when
tubes or a plate is loaded. If this occurs, remove the excess oil with a tissue or
pipettor. Do not allow oil to accumulate on the block’s top surface.
Note: The Hot Bonnet makes it unnecessary to use oil in the block, be-
cause it presses tubes into the block wells, which improves thermal contact.
Using the Slide Griddle

The Slide Griddle heats up to four glass slides for in situ protocols. Two
models are available, actively controlled and passively controlled. The
actively controlled model uses a temperature probe to allow the machine
to precisely control the Slide Griddle’s temperature. The actively con-
trolled Slide Griddle can only be used with PTC-100s that have the 60
block, since this model of the machine has a temperature probe jack. The
passively controlled model does not use a temperature probe, so it may
be used with PTC-100s that have the 96-well block or the 60 block.
See the Slide Griddle Operations Manual and Passive Slide Griddles for MJ Re-
search Thermal Cyclers for instructions on operating both types of Slide Griddle.
Using the Probe

An in-sample temperature probe is available for PTC-100s with the 60-
well block (both cold lid and Hot Bonnet models). The probe consists of a
semiconductor sensor mounted in a 0.5ml plastic tube (see fig. 2-7). A
wire runs from the sensor to the probe’s plug, which is inserted into a
jack at the back of the machine. A small amount of oil is added to the
probe tube, to serve as the representative sample. The tube is loaded into
the block, where it can serve as the control reference for any programmed
target temperature between 4 and 96°C.
When a probe-control protocol is run, the PTC-100 controls the block’s
temperature to keep the probe at the programmed temperature, using
feedback information from the sensor. Protocols must be tailored to fit
this control mechanism (see chapter 6).
Customizing the Probe Vessel

For the most precise control of sample temperatures, install the probe
sensor in the same type of tube that the samples will be placed in. This is
4-10
Operation
particularly important when the sample tubes have much thicker walls
than the probe’s tube.
Follow these steps to customize the probe vessel:
1. Uncap the probe tube. The sensor will come out when the lid is removed.
2. Remove the lid from the new probe tube. Add oil to the probe tube as
described below under “Adding the Oil.”
3. Gently place the sensor in the new tube, and snap the lid closed. Make
sure that the lid from the original probe tube fits the new tube tightly
and that the tube is long enough to accommodate the sensor wire.
The sensor should rest on the bottom of the tube.
Caution: The sensor and the wires connecting it to the probe are
fragile. Handle them with great care. In particular, do not
bend the wires connecting the sensor to the main probe
wire.
Adding the Oil

Viscous oils (not water!) are the best choice for the probe tube’s represen-
tative sample. They closely mimic the thermal characteristics of buffer
solution, which changes temperature sluggishly due to the high specific
heat of water.
Light and heavy mineral oil and silicone oil may be used (Table 4-1). MJ
RESEARCH recommends using heavy mineral oil because the formula for
determining the correct volume of oil to use is easy to remember, and it is
widely available and inexpensive. But whichever type of oil you use, be
careful to add the correct amount of oil.
Table 4-1 Calculating the correct amount of oil
Type of oil Sigma number Amount to use

Heavy mineral oil 400-5 1 x volume of buffer in individual sample tube
+ 1 x volume of oil overlay
Light mineral oil M5904 1.4 x volume of buffer in individual sample tube
Silicone oil DMPS-5X 1.7 x volume of buffer in individual sample tube
Silicone oil DMPS-V 2.7 x volume of buffer in individual sample tube
4-11
Loading and Connecting the Probe

Seat the probe tube in the center of the block. If oil is used to thermally
couple samples to the block, it must also be used on the probe tube.
Plug the probe into the jack at the back of the instrument (see fig. 2-2).
Close the lid, making sure that the probe wire exits the lid through the
small hole provided for it.
When the probe is connected to the machine, the probe calibration screen
will be displayed every time Run Program is selected from the Run-Enter
menu (see “Calibrating the Probe,” below).
Running a Protocol under Probe Control

To run a protocol under probe control, load and connect the probe as
described above. Select a protocol that has been designed for probe con-
trol and press «Proceed». The following screen will be displayed:
In-sample Probe
Control? _NO Yes
Select Yes and press «Proceed». The protocol will begin running under
probe control.
Calibrating the Probe

Calibrate the probe for the following conditions:
• the first time it is used and once a month thereafter
• whenever there is a discrepancy of 1°C or more between block tempera-
ture and probe temperature at a steady-state, near-ambient temperature
• whenever it takes longer than 20 seconds for the block to equilibrate
at a new temperature, when running a probe-control program
For greatest accuracy, recalibrate the probe whenever the sample volume
changes.
To calibrate the probe, remove all samples from the block. Fill the probe
with enough oil to completely cover the sensor. Firmly seat the probe in
the center of the block, and plug it into the machine. Close the machine’s
lid, select a program, and press «Proceed». The following screen will be
displayed:
Calibrate Probe?
N/Y Takes 10 Min
4-12
Operation
Select Y and press «Proceed». The following screen will be displayed:
REMOVE YOUR
SAMPLES
Remove all samples from the block, then press «Proceed». The following
screen will be displayed:
Check Probe Prep

Insert in Block_
If the probe is filled with the correct amount of oil and inserted into the
block, press «Proceed». The calibration process will begin. The machine
will cool the probe sample to 4°C for 3 minutes, then heat it to 96°C for 3
minutes. A screen will be displayed during the calibration, showing the
block temperature in the upper right-hand corner and the probe tem-
perature in the lower right-hand corner:
CALIBRATING 23.2
24.5
When the calibration is completed, you may load samples and run a protocol.
4-13
Appendix 4-A Tube, Microplate, and Sealing

System Selection Chart
Key
● Reaction vessel fits block without modification.
❍ Reaction vessel must be cut to fit.
MJ RESEARCH Thermal Reaction Vessels Sealing Options for Oil-Free Cycling

Cycler Blocks
96V 60 16 slide Description MJ RESEARCH Microseal Microseal 8-Strip 12-Strip Self-Seal Frame-Seal
(0.2ml) (0.5ml) 'A' film 'M' mat* caps caps reagent chambers
Catalog # MSA-5001 MSM-1001 TCS-0801 TCS-1201 SLR-0101 SLF-series
● Multiplate 96-well microplates MLP-9601 ● ● ● ●
● Multiplate 48-well microplates MLP-4801 ❍ ●* ● ❍
● Multiplate 24-well microplates MLP-2401 ❍ ●* ● ❍
● Multiplate 25-well microplates MLP-2501 ❍ ●* ❍ ❍
● Concord 96-well microplates CON-9601 ●
● 8-strip 0.2-ml tubes TBS-0201 ● ●* ● ❍
● 12-strip 0.2-ml tubes TBS-1201 ● ●* ❍ ●
● 0.2-ml tubes, no caps TBI-0201 ● ●* ● ●
● 0.2-ml tubes w/caps TWI-0201

● 0.5-ml tubes w/caps, thin wall TBI-0501
● 0.5-ml tubes w/caps, thick wall TBI-0601
● Glass slides SLS-series ● ●
* Microseal ‘M’ and ‘P’ sealers are sized for 96-well blocks but can be used with fewer than 96
wells if the vessels are positioned symmetrically in the block.
Note: All tubes and Multiplate microplates are made from polypropylene plastic, the optimal
material for this application. “Concord” microplates are made from polycarbonate plastic, which
exhibits some vapor loss through the plate walls.
4-14
Operation
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, prob-
ably SO2. 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,
0.2ml tubes, and 0.5ml tubes.
96-Well Polycarbonate Microplates

These microplates present the largest risk of contamination. Polycarbonate is somewhat perme-
able both to water and the 35S breakdown product. This problem is exacerbated when polycarbon-
ate plates are held at high temperatures for long periods of time, or when the plates are sealed for
oil-free thermal cycling.
0.2ml Polypropylene Tubes and 96-Well 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 35S breakdown
product. Either way, there have been reports of 35S passing through the walls of 0.2ml tubes of
several different brands during thermal cycling. No data are yet available on radioactive contami-
nation with polypropylene microplates.
0.5ml Polypropylene Tubes

Contamination problems are rarer with this type of tube, but instances have been reported.
The Solution
1. Substitute the low-energy beta emitter 33P in cycle sequencing. 33P nucleotides are not subject
to the same kind of chemical breakdown as 35S nucleotides, and they have not been associated
with volatile breakdown products.
2. If 35S must be used, three things will help control contamination: an oil overlay inside the
tubes, mineral oil in the thermal cycler outside the tubes, and use of thick-walled 0.5-ml tubes.
Always run 35S thermal cycling reactions in a fume hood, and be aware that vessels may be
4-15
contaminated on the outside after thermal cycling. Please be certain that you are using the
appropriate detection methods and cleaning procedures for this isotope. Consult your radia-
tion safety officer for his or her recommendations.
If mild cleaning agents do not remove radioactivity, harsher cleaners may be used. Users have
suggested the detergent PCC-54 (Pierce Chemical Co., Rockford, Illinois; Pierce Eurochemie B.V.,
Holland), Micro Cleaning Solution (Cole-Parmer, Niles, Illinois), and Dow Bathroom Cleaner (avail-
able in supermarkets).
Caution: Harsh cleaning agents are corrosive to aluminum and must never be used on bare
aluminum blocks. MJ RESEARCH blocks are anodized, so they have a protective coating
of aluminum oxide. Still, harsh agents (such as those above) must be thoroughly rinsed
away within a few minutes of application, or the anodization will degrade.
4-16
5 Running Protocols
Running a Protocol .......................................... 5-2

Running a Protocol on the PTC-100 with Hot Bonnet ..... 5-2
Running a Protocol under Probe Control ....................... 5-2
Reading the Runtime Screen ............................ 5-3
Reading the LED Bar Graph ............................. 5-3
Reading the Protocol Completion Screen ......... 5-4
Manually Stepping Through a Protocol ........... 5-4
Pausing a Running Protocol ............................. 5-4
Stopping a Running Protocol ........................... 5-5
Resuming a Protocol after a Power Outage ..... 5-5
Running an Instant Incubation ......................... 5-7
Printing a Log of a Running Protocol ................ 5-7
Printing a Record of Actual Temperatures ........ 5-8
5-1
Running a Protocol
Either a custom-designed protocol or one of the factory-installed proto-
cols may be run. See appendix C for descriptions of the factory-installed
protocols, which may be edited to fit your needs.
Select Run Program from the Run-Enter Menu, then press «Proceed».
Press one of the «Select» keys until the name of the protocol you wish to
run is displayed, then press «Proceed». The protocol will begin running.
Run
QUIKSTEP?
Running a Protocol on the PTC-100 with Hot Bonnet

Select a protocol to run and press «Proceed». The following screen will
be displayed:
_ENABLE Disable
Heated Lid
To enable the Hot Bonnet, first make sure it is plugged into its jack (see
fig. 2-5). Select Enable and press «Proceed». The protocol will begin to
run, and the Hot Bonnet will be turned on.
Note: If the Hot Bonnet is not plugged into the machine and you enable
it and run a protocol, the machine will begin beeping.
If you do not wish to use the Hot Bonnet, select Disable and press «Pro-
ceed». The protocol will begin to run, without the Hot Bonnet.
Running a Protocol under Probe Control

To run a protocol under probe control, load and connect the probe (see p.
4-12). Select a protocol that has been designed for probe control. Do not
use probe control to run a protocol designed for block control. Press «Pro-
ceed». The following screen will be displayed:
In-sample Probe
Control? _NO Yes
Select Yes and press «Proceed». The protocol will begin running under
5-2
Running Protocols
probe control.
If probe control is not desired, select No and press «Proceed». The proto-
col will begin running under block control.
Reading the Runtime Screen

During a protocol run, a runtime screen will be displayed:
CUSTOM1 3 65.4
2 64.0
This screen lists the program name (CUSTOM1 in the example above),
the protocol step that is running (3), the block temperature (65.4°C), the
cycle number (2), and the sample temperature if the probe is installed
(64.0°C).
When the target temperature for a step is reached, a timer begins run-
ning in the middle of the second line:
CUSTOM1 3 92.0
2 00:10 92.1
The timer shows the length of time the samples have been held at the
displayed temperature. When another step begins, the timer disappears
until the new step’s target temperature is reached. At that point the timer
begins running for the step.
Reading the LED Bar Graph

As the protocol runs, the LED bar graph indicates how much power is
going to the block’s heat pump. The upper half of the bar lights up red
5-3
when the block is heating, and the lower half lights up green when the
block is cooling. The percentage of the column that lights up during ei-
ther heating or cooling provides an instantaneous reflection of how much
energy the heat pumps are using to either heat or cool the block.
Reading the Protocol C ompletion Screen

When the protocol ends, a beeper sounds and a message is displayed:
CUSTOM1 3 92.0
COMPLETE
The temperature of the block at the completion of the program is dis-

played in the upper right-hand corner of the screen. The number will
change as the block cools to ambient temperature.
Press «Proceed» to remove this screen. The Run-Enter Menu will be dis-
played, and another protocol may be run.
Manually Stepping Through a Protocol

A running protocol can be manually advanced through its steps. As soon
as a step has reached its target temperature (i.e., when the timer begins
running for the step), press «Proceed» to progress the protocol to its next
programmed step. The next protocol step will immediately be displayed.
Note: Pressing «Proceed» while a step is ramping will have no effect.

A step must reach its target temperature before the protocol can be manu-
ally advanced to the next step.
Protocols can be programmed to require manual stepping (see p. 6-10).
Pausing a Running Protocol

Press «Pause» to temporarily stop a running protocol. If «Pause» is
pressed during temperature ramping, the protocol will pause as soon as
the target temperature is reached, and samples will be held at the dis-
played temperature. If «Pause» is pressed after a step has reached its
target temperature, the protocol will immediately begin holding samples
5-4
Running Protocols
at the current incubation temperature. The timer will stop running, and
the word “Pause” will be displayed:
CUSTOM1 3 92.0
2 PAUSE
To resume the protocol, press «Pause» again. The timer will begin run-
ning again, and the protocol will complete the step that was paused and
continue on to the next step.
Stopping a Running Protocol

Press «Stop» or «Cancel» to stop a running protocol. A beeper will sound,
and the program will stop running. The program cancellation screen will
be displayed:
CUSTOM1 2 75.2
CANCELED BY USER
The current block temperature is displayed in the upper right-hand cor-

ner of this screen. The reading will change as the block returns to ambi-
ent temperature. Press «Proceed» to remove this screen. The Run-Enter
Menu will be displayed.
Note: Turning off the machine will not cancel a running protocol. Instead,
the PTC-100 will assume that a power outage has occurred and will resume
the protocol run when the machine is turned on again (see below).
Resuming a Protocol after a Power Outage

If a power failure occurs when a protocol is running, the PTC-100 will
hold the protocol in memory for at least 24 hours and sometimes up to 10
days. (The exact duration depends on environmental conditions.)
When power is restored, the protocol will begin running again at the
point at which it was stopped. When the protocol ends, the protocol
completion screen will be displayed, with a special notice on its last line:
CUSTOM1 Complete
PRESS PROCEED
5-5
Press «Proceed» as instructed. A screen about the power outage will be

displayed. The screen will identify the step and the cycle that were run-
ning when the power failure occurred:
AC POWER FAILED
Cyc 3 Step 2
Press «Proceed» to remove this screen. The Run-Enter Menu will be dis-
played again.
Running an Instant Incubation

The PTC-100 may be converted to a constant-temperature incubator by press-
ing «Instant» (the zero key) while the Run-Enter Menu is displayed. A screen
allowing entry of the incubation temperature will be displayed:
TEMP:_
Type any incubation temperature from 0.0°C to 100.0˚C, then press «Pro-
ceed». The PTC-100 will incubate the sample at the specified temperature.
When the block reaches the incubation temperature, a timer will begin
running in the lower right-hand corner of the screen. To stop and start
the timer, press «Pause». To stop an instant incubation, press «Cancel»
or «Stop» (see “Stopping a Running Protocol”).
Printing a Log of a Running Protocol

If the PTC-100 is connected to a printer, it will print a log for a running
protocol that includes
• The machine’s serial number and software version
• The hours of operation and calibration data
• The protocol’s name and a list of its steps
• The protocol’s temperature control method
• The runtime thermal data from the block and from the probe if it is
installed
See “Printing a Program,” chapter 6, for information about compatible printers.
5-6
Running Protocols
Printing a Record of Actual Temperatures

A 0–5 VDC strip chart recorder may be used to print a graph of the
temperature of the sample block over time, derived from the thermal
sensor on the block.
To use the chart recorder, plug a miniature phone plug patch cord (3/32-
inch twin conductor) into the chart recorder jack on the left side of the
PTC-100 (fig. 2-2). Connect the other end to a chart recorder, being cer-
tain to observe correct polarity (the tip is positive).
Suitable chart recorders may be obtained from the following companies:
Gulton Graphic Instruments
1900 South County Trail
East Greenwich, RI 02818
Phone: 401-884-6800
Fax: 401-884-4872
Model: 288
Omega Engineering
PO Box 4047
Stamford, CT 06907
Phone: 800-826-6342
Fax: 203-359-7700
Model: RD288-5V-15IN
Kipp & Zonen
390 Central Avenue
Bohemia, NY 11716
Phone: 800-645-1025
Fax: 516-589-2068
Model: BD111
The Gulton and Omega machines have an accuracy of only ± 2% of span
(i.e., less than ± 2°C), so they should only be used for event verification, not
actual measurement. Kipp & Zonen’s laboratory-grade flatbed machine has
an accuracy of 0.3% of span, so it may be used for temperature measure-
ment as well as event verification. However, calibration of output vs. tem-
perature is still necessary. The Kipp & Zonen machine also has an optional-
purchase feature allowing digital output of temperature data through a se-
rial port, so that data may be downloaded into a computer.
5-7
5-8
6 Programming
The Elements of a Program ......................... 6-2 Editing While Entering a Program ............... 6-11
Changing the Last Value Entered or Last
Desigining a New Program ........................ 6-2 Menu Option Chosen .................................. 6-11
Translating a Protocol into a Program ..................... 6-2 Changing All Values in the Step Being Entered ....... 6-11
Using the GoTo Step to Write Short Programs ......... 6-2 Changing Values in Earlier Steps of a Program
Choosing a Temperature Control Method ............... 6-3 Being Entered .............................................. 6-11
Block Control .................................................... 6-3
Probe Control ................................................... 6-3 Deleting an Incomplete Program ................ 6-12
Entering a New Program ............................ 6-4 Deleting a Program from Memory ............. 6-12
Initiating the Program .............................................. 6-4
Naming the Program ............................................... 6-5 Listing a Program ....................................... 6-12
Entering the Program Steps ..................................... 6-5
Entering a Temperature Step ............................ 6-5
Printing a Program ..................................... 6-13
Entering a GoTo Step ....................................... 6-6
Entering an Increment Step .............................. 6-7
Entering an Extend Step ................................... 6-8 Keeping a Permanent Record of Programs ... 6-14
Entering a Slope Step ....................................... 6-9
Entering the End Step ....................................... 6-10
Programming an Indefinite Hold ................ 6-10
Creating a Program That Requires Manual

Stepping .......................................... 6-10
6-1
The Elements of a Program

PTC-100 programs consist of a series of steps encoding a protocol. These
steps are run using one of two temperature control methods: block con-
trol or probe control.
Programs may contain six types of steps. Two of the step types are man-
datory, and four are optional:
1. Temperature step (mandatory): Sets a temperature for the block and the
length of time it is held at that temperature. The PTC-100 brings the
block to this temperature at its maximum rate of heating or cooling,
unless modifying instructions are added to the program. (See chapter 2,
“Specifications,” for rates of heating and cooling for all block types.)
2. GoTo step (optional): Causes the program to cycle back to an earlier
step for a specified number of times (up to 9,999 times).
3. Increment step (optional): Allows a progressive increase or decrease
of temperature (–0.1° to 6.0°C/cycle) each time a step is executed in a
GoTo cycle (useful in “touchdown” programs, when the optimal an-
nealing temperature of an oligonucleotide is not known).
4. Extend step (optional): Allows a progressive lengthening or short-
ening of a temperature step hold (by 1–60 sec/cycle) each time a step
is executed in a cycle (useful for accommodating an enzyme with
diminishing activity).
5. Slope step (optional): Allows a slower-than-maximum rate of heat-
ing or cooling.
6. End step (mandatory): Instructs the PTC-100 to shut down its heat
pump because the last line of the program has run.
Designing a New Program

Translating a Protocol into a Program
Until you are completely familiar with programming the PTC-100, you
may find it helpful to first translate the protocol into program steps on
paper. Write down the protocol to be programmed, one step per line.
Then write the type of program step that goes with the protocol steps, at
the end of each line. Finally, write the End step at the bottom of the list;
programs will not run without this step. Number the lines 1 through N,
where N is the final, End line.
Using the GoTo Step to Write Short Programs

The GoTo step allows programs of many repeated steps to be shortened
to just a few lines. When the program encounters a GoTo step, it returns
6-2
Programming
to a specified step, repeats that step, and repeats all steps that follow,
back to the GoTo step. When the program has returned, or cycled, back
to the step a specified number of times, the program moves on to the step
that follows the GoTo step.
For example, consider a basic cycle sequencing protocol consisting of 30
repeats of the denaturation and annealing/extension steps. Rather than
listing all 60 steps, use a GoTo step to design a short, easy-to-enter pro-
gram:
Raw program: Shortened program:

1. 92° for 30 sec 1. 92° for 30 sec
2. 60° for 3 min 2. 60° for 3 min
3. 92° for 30 sec 3. GoTo step 1, 29 times (i.e., cycle
4. 60° for 3 min back to step 1 and repeat steps 1
5. 92° for 30 sec and 2, 29 times )
6. 60° for 3 min 4. End
7. 92° for 30 sec
[continues for total of 60 lines]
Choosing a Temperature Control Method

The PTC-100 can control block temperature in two ways, each of which
has different implications for the speed and accuracy of sample heating:
• Block control: The PTC-100 adjusts the block’s temperature to main-
tain the block at programmed temperatures, independent of sample
temperature.
• Probe control: The PTC-100 adjusts the block’s temperature to main-

tain the probe at programmed temperatures.
Block Control
Block control is available for all models of the PTC-100. Under block con-
trol, the temperature of samples always lags behind the temperature of
the block. The duration of this time lag depends on the sample vessel
and sample volume but typically is between 10 and 30 seconds.
Probe Control
Probe control is available for PTC-100s equipped with the 60 block. Spe-
cial care must be taken to fill the probe with the correct amount of oil and
to seat the probe and the samples correctly. Otherwise, actual sample
temperatures can vary widely from the probe’s temperature. Probe con-
trol cannot be used with microplates or slides.
Under probe control, the machine will slightly overshoot its heat targets
6-3
to account for the time required for heat to transfer to the sensor within
the probe tube. Therefore, probe control protocols typically require incu-
bations that are 15–20 seconds shorter and 1–2°C lower than incubations
for block control protocols. For example, a denaturation step in a block-
control protocol calling for 94°C for 30 sec would be reduced to 92°C for
10 sec in a probe-control protocol.
✔ Tip: Block control programs tend to be more trouble-free than probe

control because fewer variables are involved in the tempera-
ture control feedback loop.
Entering a New Program

Programming the PTC-100 involves four steps:
1. Initiating the program
2. Naming the program
3. Entering the program’s steps
4. Entering the End step
Each step involves typing in values from the keyboard or making selec-
tions from a menu. Programs may be edited as they are being entered or
after they have been stored. Programs are automatically saved when the
End step is entered.
Initiating the Program

To initiate a new program, select Enter Program from the Run-Enter Menu,
then press «Proceed». The Main Menu will be displayed:
_NEW List
Edit Delete
Select New, then press «Proceed». The naming screen will be displayed:
Name A
6-4
Programming
Naming the Program

Program names may be up to eight characters long and may consist of
any combination of letters (Roman and Greek), numbers, punctuation
marks, or Japanese Katakana.
Press the right «Select» key to scroll forward and the left «Select»
key to scroll backward through the alphabets and characters avail-
able, which are presented in this order: Roman alphabet, selected
Greek letters, punctuation marks, numbers. To access the Japanese
Katakana syllabary, press the «.» key. A second press of «.» returns the
machine to Western characters.
When the character needed is displayed next to Name, press «Proceed».
The character will be accepted, and the cursor will move one space to the
right. Numbers and dashes may also be inserted by pressing the corre-
sponding keys on the keypad.
When the name is complete, press «Proceed» once to enter the last char-
acter and again to enter the whole name. If the name is already in use for
a program, a screen saying “Name In Use” will be displayed. If this hap-
pens, press «Proceed», then enter a different name.
Entering the Program Steps

When the name has been entered (CUSTOM1 is used in the following
examples), the Enter Menu will be displayed:
Step 1 _TEMP
Goto Option End
Use this menu to enter each step of the program:

• Temp enters a temperature step.
• GoTo enters a GoTo step.
• Option enters an increment, extend, or slope step.
• End enters the End step.
Entering a Temperature Step

To enter a temperature step, select Temp from the Enter Menu, then press
«Proceed». The first Temp screen will be displayed:
Step 1
Temperature _
6-5
The first line of this screen shows the number of the step being pro-
grammed (1 is used in the example above). The second line of the screen
allows a target temperature (in degrees Celsius) to be entered for the
step. Type any number between 0 and 100.0 as the target temperature
(92.5 is used in the example below):
Step 1
Temperature 92.5
Press «Proceed». The temperature will be accepted, and a screen allow-

ing entry of an incubation time will be displayed:
Step 1 Hrs _
Min Sec
A value must be entered for Hrs (hours), Min (minutes), and Sec (seconds).
Use the «Select» keys to move the cursor to each option, and either type a
number or press «Proceed» to automatically enter a value of 0.
For example, to enter an incubation time of 30 seconds, press «Proceed»
twice. The value of 0 will automatically be entered for Hrs and Min, and
the cursor will be positioned at Sec. Use the keyboard to type “30.” The
screen will look like this:
Step 1 Hrs 0
Min 0 Sec 30_
Press «Proceed». The times will be accepted, and the Enter Menu will be
displayed again. Use the Enter Menu to add another step to the program.
Entering a GoTo Step

To enter a GoTo step, select GoTo from the Enter Menu and press «Pro-
ceed». The first GoTo screen will be displayed:
Step 2
Go to step _
6-6
Programming
The first line of this screen shows the number of the step being pro-
grammed (2 is used in the example above). The second line of the
screen allows entry of the number of the step the program should
cycle back to.
Type the number of the step the program should cycle back to (1 is used
in the example below):
Step 2
Go to step 1
Press «Proceed». The number will be accepted, and a screen allowing

entry of an additional number of cycles will be displayed:
Step 2 Go to 1
_ more times
Type the additional number of times the program should cycle back to
the step (24 is used in the example below):
Step 2 Go to 1
24 more times
Press «Proceed». The number will be accepted, and the Enter Menu
will be displayed again. Use the Enter Menu to add another step to
the program.
Entering an Increment Step

To enter an increment step, select Option from the Enter Menu and press
«Proceed». The Options Menu will be displayed:
Step 3 _EXTEND
Increment Slope
Select Increment and press «Proceed». A screen allowing entry of the ini-
tial incubation temperature for the step will be displayed:
Step 3
Temperature _
6-7
Type a temperature and press «Proceed». The number will be accepted,

and a screen allowing entry of an incubation time will be displayed:
Step 3
Min _ Sec
Type a number for Min and Sec. Press «Proceed» to automatically enter a
value of 0.
When the numbers have been typed, press «Proceed». The numbers will
be accepted, and a screen allowing entry of a temperature increment or
decrement will be displayed:
Step 3
Add _ ° /cycle
Type a temperature from –0.1 to 6.0°C (the maximum programmable

range) as the number of degrees by which the incubation temperature
will increase or decrease each time the step is executed in a cycle. Incre-
ments as small as one tenth of a degree may be used. Use a negative
number to program a progressive decrease of temperature, and a posi-
tive number to program a progressive increase.
When the number has been typed, press «Proceed». The number will be
accepted, and the Enter Menu will be displayed again. Use the Enter Menu
to add another step to the program.
Entering an Extend Step

To enter an extend step, select Option from the Enter Menu and press
«Proceed». The Options Menu (see above) will be displayed. Select Ex-
tend and press «Proceed». Type the initial incubation temperature and
incubation time as for an increment step (see above), and press «Pro-
ceed». The temperature and time will be accepted, and a screen allowing
entry of a time increment or decrement will be displayed:
Step 4
Extend _ S/cyc
Type a number from –60 to 60 (the maximum programmable range) as

the number of seconds by which the incubation time will increase or de-
crease each time the step is executed in a cycle. Use a negative number to
program a progressive decrease of incubation time, and a positive num-
ber to program a progressive increase.
6-8
Programming
When the number has been typed, press «Proceed». The number will be
accepted, and the Enter Menu will be displayed again. Use the Enter Menu
to add another step to the program.
Entering a Slope Step

To enter a slope step, two values must be specified:
• The desired temperature change for the step: This is the difference
between the temperature of the block at the beginning of the slope
step and the desired block temperature at the end of the slope step.
For example, if the final temperature of the preceding step is 92°C
and the desired final temperature of the slope step is 65°C, the de-
sired temperature change is 27°C.
• The slope rate for the step: This is a ratio of degrees per unit of time
(usually degrees per second). Use the smallest convenient time in-
crement to achieve the smoothest temperature curve for the step. For
example, 0.1°C per second will give a smoother curve than 1°C per
10 seconds.
To enter a slope step, select Option from the Enter Menu and press «Pro-
ceed». The Options Menu (see above) will be displayed. Select Slope and
press «Proceed». A screen allowing entry of the magnitude of the tem-
perature change for the step will be displayed:
Step 4
Slope _ °
Type a number for the desired temperature change and press «Proceed».
The number will be accepted, and a screen allowing entry of the rate of
heating or cooling will be displayed:
_ ° per Hrs
Min Sec
Type a temperature from 0.1 to 1.5°C (the maximum programmable range)

for the numerator of the slope rate and press «Proceed». The tempera-
ture will be accepted, and the cursor will move to Hrs. Type a time value
for the denominator of the slope rate. A number must be entered for Hrs,
Min, and Sec. Press «Proceed» to automatically enter a value of 0 and
move the cursor to the next time element.
When the denominator has been typed, press «Proceed». The num-
bers will be accepted into the program, and the Enter Menu will
be displayed again. Use the Enter Menu to add another step to the
program.
6-9
Note: Not all blocks will be able to ramp at the maximum program-
mable speed of 1.5°/sec. See chapter 2, “Specifications,” to determine the
maximum speed possible for a given block.
Entering the End Step

To enter the End step, select End from the Enter Menu, then press «Pro-
ceed». A confirmation screen will be displayed:
Step 6
End
Press «Proceed». The End step will be entered into the program. The
program will be stored, and the Run-Enter Menu will be displayed.
Programming an Indefinite Hold

Programs can be designed to end in an indefinite hold at a specified tem-
perature. This allows completed reaction products to be held at a stable
refrigeration temperature (often 4°C) at the end of a run, until they can
be conveniently removed.
To program an indefinite hold, program a temperature step immedi-
ately before the protocol’s End step. Type the desired temperature for
the indefinite hold, then give the step an incubation time of 0 hours, 0
minutes, and 0 seconds. When this temperature step is reached, the
block will heat or cool the samples to the desired temperature and
hold them there until you manually end the program by pressing
«Cancel» or «Stop».
Creating a Program That Requires Manual Stepping

To create a program that must be manually progressed to each step, pro-
gram an indefinite hold for each temperature step in the protocol (see
“Programming an Indefinite Hold,” above). When the protocol runs, you
may then advance it through its steps at the time desired.
6-10
Programming
Editing While Entering a Program
Changing the Last Value Entered or Last Menu Option

Chosen
To change the last value entered or last menu option chosen, press «Can-
cel». The choice just made will be cancelled, and another value may be
entered or another menu option chosen. Press «Proceed» after changing
a value, so that the program will accept it.
Changing All Values in the Step Being Entered

To change all the values in the step currently being entered, repeatedly
press «Cancel». Each time you press the key, the cursor will move back-
ward through the step’s values, deleting them as it moves. When all val-
ues for the step have been deleted, enter new values, or press «Cancel»
one more time to display the Enter Menu for the step. At this point you
can change the step to a different type or re-enter the step.
Changing Values in Earlier Steps of a Program Being

Entered
To change one or more values in earlier steps of the program you are
entering, repeatedly press «Cancel» until the Enter Menu for the step
you are working on is displayed. Press «Cancel» one more time to dis-
play the last-entered step. The step will be displayed in a special format:
CUSTOM1 3 94.0
00:00:10
In the example above, the last-entered step is a temperature step. The

step number is 3, and the temperature for the step is 94.0°C. The incuba-
tion time is displayed in the form of 00:00:00. The first two digits repre-
sent hours, the second two digits represent minutes, and the last two
digits represent seconds. The step in the example is programmed for a
10-second incubation.
At this point you may use the arrow keys to scroll through the program’s
steps. To change temperature, time, and cycling values, see chapter 7.
Note: You cannot change the program name, step number, or step type.
To change the program’s name or the order or type of its steps, delete the
program (see below) and then re-enter it.
6-11
After you have made all necessary changes, press the right «Select» key
until the Enter menu is displayed for the next step in the program. Con-
tinue entering the new program.
Deleting an Incomplete Program

To delete a program that you are in the process of entering, enter the End
step and press «Proceed», which will store the program. Then delete the
program from memory (see below).
Deleting a Program from Memory

To delete a program, select Enter Program from the Run-Enter Menu and
press «Proceed». The Main Menu will be displayed. Select Delete and
press «Proceed». The deletion screen will be displayed for the first pro-
gram in memory:
Delete
CUSTOM1?
Press the «Select» keys until the name of the program to be deleted is
displayed. When the correct name is displayed, press «Proceed». The
program will be deleted, and the Run-Enter Menu will be displayed.
Listing a Program
Use the List option on the Main Menu to display all of a program’s steps
in the LCD window. To enter List mode, select Enter Program from the
Run-Enter Menu and press «Proceed». The Main Menu will be displayed.
Select List and press «Proceed».
Press the «Select» keys until the name of the program to be listed is dis-
played, then press «Proceed». The first step in the program will be dis-
played in the LCD window. Press the right «Select» key to scroll forward
and the left «Select» key to scroll backward through the list of steps. To
exit List mode, scroll to the last step of the program, then press the right
«Select» key once. The Run-Enter Menu will be displayed.
Note: No program values can be changed in List mode. To change pro-

gram values, see chapter 7 .
6-12
Programming
Printing a Program
The PTC-100 can print all the programs stored in the machine. To do this,
follow the instructions under “Listing a Program” to enter List mode. If a
printer is connected to the printer port, the List program screen will give
you the option to print as well as list programs in the LCD window:
_DISPLAY Program
Print Programs
Select Print Programs and press «Proceed». Each program stored in the ma-
chine will be printed.
The PTC-100 parallel printer port is compatible with Epson® LX-810 dot
matrix printers and many other IBM compatibles. Only printers that sup-
port the Epson extended graphics set will be able to print the degree charac-
ter (°). Other printers will print an x instead of the degree character.
Keeping a Permanent Record of Programs

Occasionally in the course of repairing a PTC-100, it is necessary to replace
the chip that stores all custom user protocols. To avoid losing your protocols
in such an event, always maintain an up-to-date record of them. Protocols
may be printed out as described above or copied into a notebook.
6-13
7 Editing Programs
Initiating Editing .......................................... 7-2
Editing the Program .................................... 7-2

Editing Temperatures and Cycling Values ................. 7-2
Editing a Time Value ................................................. 7-3
Editing a Slope Step ................................................. 7-4
7-1
Initiating Editing
To edit an existing program the machine must be in Edit mode. To enter
Edit mode, select Enter Program from the Run-Enter Menu and press «Pro-
ceed». The Main Menu will be displayed. Select Edit from the Main Menu
and press «Proceed». A screen similar to the following will be displayed:
Edit
CUSTOM1?
The machine is now in Edit mode. Use the «Select» keys to select the
program you wish to edit. When the name of the desired program is dis-
played, press «Proceed». The first step in the program will be displayed:
CUSTOM1 1 94.0
00:00:20
The programmed temperature for this step is 94.0°C. The incubation time is
displayed in the form of 00:00:00. The first two digits represent hours, the
second two digits represent minutes, and the last two digits represent sec-
onds. The step in the example is programmed for a 20-second incubation.
Editing the Program

Press the left «Select» key to scroll backward through the program steps,
and the right «Select» key to scroll forward. As the left or right «Select»
key is pressed, the cursor will progressively move backward or forward
through each value in a step, and then back to the preceding or forward
to the following step.
Editing Temperatures and Cycling Values

To change a temperature or a cycling value, position the cursor on it and
type the new value. Press «Proceed». The new value will be accepted,
and the cursor will move forward to the next value in the step.
To cancel a change, press «Cancel». The just-typed value will disappear,
and a blank line will be displayed in its place. Type a new value and
press «Proceed».
7-2
Editing Programs
Note: Be careful when editing program values. Once a value is changed

or deleted, you cannot make it reappear by pressing any key. To restore a
value, you must retype it. You may find it helpful to write a value down
before changing it, to minimize the chance that you will forget what it was.
Editing a Time Value

To edit any part of a time value, you must retype the number for each
element in the time value: hours, minutes, and seconds. Press «Proceed»
after typing each time element. The number just typed will be accepted,
and the cursor will move to the next time element. To enter a value of 00
for hours, type a zero, then press «Proceed». The second zero will auto-
matically be entered. To enter a value of 00 for minutes or seconds, sim-
ply press «Proceed». Both zeros will be entered at once.
For example, to change the time value for the example above from 00:00:20
to 00:00:30, press the right arrow key to move the cursor to the first digit
of the time value:
CUSTOM1 1 94.0
00:00:30
Type a zero. The zero will become the first digit of the hours element, and
the values for minutes and seconds will disappear from the screen:
CUSTOM1 1 94.0
0 : :
Press «Proceed». A second zero will automatically be entered for the hours
element, and the cursor will move to the minutes element:
CUSTOM1 1 94.0
00:_ :
Press «Proceed». Two zeros will automatically be entered for the min-
utes element, and the cursor will move to the seconds element:
CUSTOM1 1 94.0
00:00:_
7-3
Type the number 30, then press «Proceed». The number will be entered
for the seconds element, and the cursor will move back to the first digit
for the hours:
CUSTOM1 1 94.0
00:00:30
Editing a Slope Step

To edit a slope step you must retype both a sign (plus or minus) and a
number. Press «.» (the period key) to enter a plus sign and «-» (the hy-
phen) to enter a negative sign. Press «Proceed» after entering the new
slope step value.
7-4
8 Maintenance
Cleaning the Chassis and Block .................... 8-2
Cleaning the Air Vents ................................. 8-2
Cleaning Radioactive or Biohazardous

Materials Out of the Block ............... 8-2
Changing the Fuses ..................................... 8-2
8-1
Cleaning the Chassis and Block

Clean the outside of the PTC-100 with a damp, soft cloth or tissue when-
ever something has been spilled on it or the chassis is dusty. A mild soap
solution may be used if needed.
Clean the block’s wells whenever anything is spilled into them or when
the oil in them is discolored or contains particulate matter. It is particu-
larly important to prevent the buildup of old, dirty oil, which will inter-
fere with vessel seating and diminish thermal coupling of sample vessels
to the block.
Clean the wells with a swab moistened with water, 95% ethanol, or, if a
thorough cleaning is needed, a 1:100 dilution in water of 5.25% (0.7M) so-
dium hypochlorite (household bleach). If using sodium hypochlorite, swab
the wells with water afterward to remove all traces of it. Do not clean the
block with caustic or strongly alkaline solutions (e.g., strong soaps, ammo-
nia, sodium hypochlorite at a higher concentration than specified above).
These can damage the block’s protective anodized coating.
Note: See appendix A for information on cleaning the 16 MS Slide Block.
Cleaning the Air Vents

Clean the air intake and exhaust vents with a soft-bristle brush, a damp
cloth, or a vacuum cleaner whenever dust is visible in them. If these vents
become clogged with dust and debris, airflow to the PTC-100’s heat sink
is hampered, eventually causing overheating and shutdowns (see “Air
Supply Requirements,” chapter 3).
Cleaning Radioactive or Biohazardous Materials Out of

the Block
When cleaning machines that have been running radioactive or
biohazardous reactions, consult your institution’s radiation safety officer
or biosafety officer regarding methods, monitoring, and disposal of con-
taminated materials.
Changing the Fuses

The circuits in the PTC-100 are protected by two fuses. When a fuse blows,
the PTC-100 immediately shuts down and cannot be turned back on. The
8-2
Maintenance
machine records the event as a power loss, so if a protocol is running

when a fuse blows, the machine will resume the protocol run when the
fuse is replaced and power restored (see “Resuming a Protocol after a
Power Outage,” chapter 5).
Warning: The PTC-100 incorporates neutral fusing, which means that

live power may still be available inside the unit even when
a fuse has blown or been removed. Never open the PTC-
100. You could receive a serious electrical shock. Opening
the unit will also void your warranty.
Follow this procedure to change a fuse:

1. Move the power switch to the “0” (off) position. Disconnect the power
cord from the back of the machine.
2. Insert one corner of a small flat-head screwdriver into the slot at the
left side of the fuse block (fig. 8-1A). Gently pry the block loose, and
pull it down and out. The fuses will be visible (fig. 8-1B).
3. Remove the fuses and examine them. A flat-head screwdriver may be
used to pry the fuses loose, if necessary. A broken central wire or dark-
ened glass indicates that a fuse has blown and should be replaced.
4. Gently press the fuse block back into place, and reconnect the power
cord.
Figure 8-1 Changing a fuse.
A B
8-3
9 Troubleshooting
Error Messages ........................................... 9-2
Problems Related to Protocols ..................... 9-3
Problems Related to Machine

Performance ................................... 9-5
9-1
Error Messages
Error Message Cause Action

Check Block Sensor Block's temperature sensor or sensor Block may need servicing. Contact MJ
circuitry is malfunctioning. RESEARCH or your distributor.
Heat Pump Not Heat pump is not working, so Base needs servicing. Contact MJ
Functioning machine has shut down. RESEARCH or your local distributor.
HS Overheating, Machine is not getting enough air, Ensure machine is at least 10cm away
Check Air Flow or air being taken in is not cool from walls and other thermal cyclers.
enough. Make sure air being taken in is cool
(see chap. 3). If message persists, base
may need servicing; contact MJ
RESEARCH or your distributor.
Memory Full Memory has reached its capacity of Delete programs as necessary to free
1600 steps among all stored memory.
programs.
Missing Calibration A memory failure has caused Contact MJ RESEARCH or your distributor.
machine to lose block calibration.
Missing Probe Follow correct probe calibration Turn machine off, then on again, and
Calibration procedure (see p. 4-12). run protocol again. If message persists,
contact MJ RESEARCH or your distributor.
Probe Input Probe needs recalibration or is Recalibrate probe (see p. 4-12). If
Not Valid defective. message persists, probe may need
replacing. Contact MJ RESEARCH or your
distributor.
Service Heat Heat pump is malfunctioning and Base needs servicing soon, before heat
Pump Soon need servicing. pump stops working completely.
Contact MJ RESEARCH or your distributor.
Service Heat Heat pump needs replacing. Contact MJ RESEARCH or your distributor.
Pump Now
9-2
Troubleshooting
Problems Related to Protocols
Problem Cause Action

Reaction is working but "Primer-dimer" material often produces If obtaining appropriate reac-tion
broad low mole-cular a broad band in the <100bp region product/s, no need to change
weight band is seen in of gels. anything.
gels.
Minimize "primer-dimer" production
by designing primers with no 3'
self-complementarity.
Reoptimize magnesium concen-
tration and annealing temper-ature
to maximize desired pro-duct and
minimize "primer-dimers."
Reaction working but Nonspecific hybridization occur-ring Program a hot start into the
unexpected extra during setup. protocol.
products or smear is
seen.
Reaction component concentration too Check concentrations of compo-
high or too low. nents. May need to reoptimize
magnesium concentration.
Annealing temperature too low. Reoptimize annealing temperature.
Protocol contains a wrong value. Use List to check protocol's
temperature control method,
temperatures, and times.
Template not of sufficient purity. Check extraction and purifi-cation
protocols. Add additional
purification steps if necessary.
Multiple templates or host DNA in Check nucleic acid preparations by
sequencing reactions. gel electrophoresis.
(Continued)
9-3

No reaction products Wrong protocol used. Re-run reaction using correct
obtained. protocol.
Protocol contains a wrong value. Use List to check protocol's
temperature control method,
temperatures, and times.
Reaction component omitted from Check reaction assembly proto-col,
mixture. ensuring that mixture con-tains
appropriate components in correct
concentrations.
Denaturation temperature too low. Use 92° C for denaturation.
Annealing temperature too high for Check for appropriate anneal-ing
primers. temperatures of primers, using
available computer pro-grams or
empirical testing.
Wrong temperature control method Use List to check temperature
used. control method for protocol;
change if needed.
Probe failed, causing machine to run Check screen for probe failure
protocol under block control. error message. Probe may need
servicing or replacing. Call MJ
RESEARCH or your local distri-butor.
Probe not filled with correct amount Fill probe tube with correct amount
of oil. of oil (see p. 4-11).
Reaction mix contains an inhibitor "Spike" a complete reaction mix
(e.g., heme from blood). with a control template and primer
set.
Reaction vessels not making good Use only high-quality tubes/plates
thermal contact with sample block. that fit block snugly. Ensure that
wells are free of foreign materials
that would interfere with tube/plate
seating.
9-4
Troubleshooting
Problems Related to Machine Performance
Beeper sounds continu- Hot Bonnet has been enabled, but Cancel protocol. Plug Hot Bon-net
ously (PTC-100 with Hot it is not plugged into the machine. cable into its port at back of
Bonnet only). machine, and restart protocol.
Block does not heat or Heat pump is malfunctioning. Contact MJ RESEARCH or your
cool. LED bar graph is all distributor.
red or all green.
Machine will not power up. Power cable is not plugged into Make sure power cord is plugged
machine, electrical outlet is dead, into machine correctly. Make sure
or fuse has blown electrical outlet is operational.
Check fuse.
Machine starts in middle of Machine was turned off before See p. 5-5.
a protocol when turned on. protocol run had finished.
Strange characters appear LCD window or machine Reset the microprocessor by turning
in LCD window, or text in microprocessor is malfunc-tioning. machine off, then back on while
window freezes or scrolls pressing the Cancel key at the same
repe-titively. time. If problem persists, contact MJ
RESEARCH or your distributor.
9-5
Appendix A
Appendix A
The 16MS Slide Block
Description of the 16MS Slide Block

The 16MS Slide Block can thermally cycle slides and tubes. The block consists of a vertical metal
rack holding up to 16 standard 25 x 75mm slides (see fig. 2-6). Four removable thin plastic rods are
inserted into holes drilled along the back of the rack. These rods prevent loaded slides from slip-
ping out the back side of the block. Slides heat and cool uniformly as long as there is complete
contact between their bottoms and the metal slots and the block’s lid is in place.
The block can also hold 24 x 0.2ml tubes, in holes drilled into the block. This feature is useful for
optimizing primers and temperatures and running control reactions for reactions run on slides.
A wide variety of reactions done on slides may be run in the 16MS Slide Block, such as PRINS, RT-
PRINS, in situ PCR* and RT-PCR, and immunohistochemical procedures. Using Frame-Seal incu-
bation chambers to control evaporation, the slide block also may be used for precise thermal con-
trol of in situ hybridizations.
Operating the 16MS Slide Block

Selecting the Correct Sample Vessel
Suitable slides can be made of any thermally conductive material and be any shape as long as
the finished slide fits in the block’s slots. See “Selecting the Correct Sample Vessel,” chapter
4, to select tubes.
Preparing and Sealing Sample Vessels
Slides
To ensure that all samples reach the same temperatures during thermal cycling, the bottoms of
loaded slides must be in complete contact with the slots that they rest on. Do not use any slide
preparation method that would interfere with this, such as clips that extend under the slide.
Do not use mineral oil under the slides to enhance thermal contact. This is unnecessary, and the oil
is difficult to completely clean off, eventually making the slots sticky.
Use special care in sealing cover glasses or the edges of two-slide preparations (i.e., where a slide
is being used as a cover glass) with such sealers as nail polish or rubber cement. Allow the sealer
to completely dry before loading slides into slots, to avoid getting sealer on the surface of the slots
A-1
(especially a problem with two-slide preparations). Keep the bottoms of slides free of sealer, to
avoid interposing anything between the slides and the bottom of the slide slots.
Self-Seal reagent and Frame-Seal incubation chambers, available from MJ RESEARCH, are two con-
venient and effective alternatives to messy and time-consuming slide sealing methods. Other ap-
proaches to slide sealing are possible; contact MJ RESEARCH for more information.
Tubes
Since the 16MS Slide Block does not have a heated lid, tube reactions require an oil overlay.
Loading Sample Vessels into the Block
Slides
Follow this procedure to load slides into the 16MS Slide Block:
1. Inspect the block to ensure that its slots are clean and free of oil (see below for cleaning in-
structions).
2. Close off the back end of the block by inserting the small plastic rods into their holes (see fig.
2-6). This will keep the slides within their slots during loading.
3. Place slides in slots. Avoid dislodging unsealed cover glasses or the top slides in two-slide
preparations. Using a forceps can make it easier to load slides
Make sure all slides are lying flat in their slots. Remove slides that are not lying flat, clean off or
remove whatever is interfering with the slides’ seating, and re-load the slides into the block.
4. Place the removable lid over the block, to ensure that samples heat and cool uniformly.
Tubes
See “Loading Sample Vessels,” chapter 4, for instructions on loading and thermally coupling tubes
to the 16MS Slide Block. Place the removable lid over the block after tubes have been loaded, to
ensure even heating and cooling of the tubes.
Programming the 16MS Slide Block

When designing protocols for the 16MS Slide Block, remember that temperature steps must be
long enough to allow for the time required to heat the slide from the bottom to the top, where the
reactants lie. All temperature steps should be made at least 20 seconds long for all new protocols.
This length of time is sufficient to heat a typical glass slide. Once a protocol has been confirmed to
work, you may empirically test shorter temperature steps.
All programs for the 16MS Slide Block must be run under block control, as a probe is not available
for this machine.
A-2
Appendix A
Maintaining the 16MS Slide Block

Clean the 16MS Slide Block with a mild soap solution, water-based laboratory cleaner, or ethanol
(95%) and a soft cloth. Avoid strongly alkaline cleaners and chlorinated solvents. Do not immerse
the block in water.
Remove extraneous materials from slide slots with a long-handled cotton swab, small glassware
cleaning brush, or tongue depressor wrapped in laboratory tissue. Pay particular attention to clean-
ing the bottoms of slots. Remove nail polish from slots with acetone.
A-3
Appendix B
Safety Warnings
Warning: Operating the PTC-100 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 PTC-100 or any accessory to the PTC-100.
Doing so will void your warranties and can put you at risk for electrical shock.
Return the PTC-100 to the factory (US customers) or an authorized distributor (all
other customers) if repairs are needed.
Warning: The PTC-100 block 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 PTC-100 incorporates neutral fusing, which means that live power may still
be available inside the unit even when the fuse has blown or been removed. Never
open the PTC-100; you could receive a serious electrical shock. Opening the unit
will also void your warranties.
Safe Use Guidelines

The PTC-100 is designed to be safe to operate under the following conditions:
• Indoor use
• Altitude up to 2000m
• Ambient temperature 4–32°C
• Humidity 10–90%, noncondensing
• Transient overvoltage per Installation Category II, IEC 664
• Pollution degree 2, in accordance with IEC 664
• Installation category II
Electromagnetic Interference
The PTC-100 has been tested and found to comply with the limits for a Class A digital device,
pursuant to part 15 of the US FCC Rules. These limits are designed to provide a reasonable protec-
B-1
Appendix B
tion against harmful interference when the equipment is operated in a commercial environment.
This machine 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 machine in a residential area is likely to cause harmful interference, in which case the
user will be required to correct the interference at his or her own expense.
In addition, the PTC-100 design has been tested and found to comply with the EMC standards for
emissions and susceptibility established by the European Union at time of manufacture.
FCC Warning
Changes or modifications to the PTC-100 not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
B-2
Appendix C
Factory-Installed Protocols
Name Step Temperature & Time
ICEBUKET 1 4° , 0:00:00
LIGATION 1 15° , 0:00:00
37° -1HR 1 37° , 1:00:00
2 4° , 0:00:00
37° -6HR 1 37° , 6:00:00
2 4° , 0:00:00
65° 1 65° , 0:00:00
DENATURE 1 95° , 0:05:00
BOIL 1 100° , 0:05:00
CUT&KILL 1 37° , 1:00:00
2 70° , 0:05:00
C-1
Appendix D
Appendix D
Warranties
U.S. & Canadian Warranty, Standard

MJ Research, Incorporated warrants new MJ Research brand thermal cyclers (Models PTC-100,
PTC-150, PTC-200 & PTC-225) against defects in material and workmanship for a period of two
years from the date of purchase. If a defect is discovered, MJ Research, Incorporated will, at its
option, repair, replace, or refund the purchase price of the thermal cycler at no charge to the cus-
tomer, provided the product is returned to MJ Research, Incorporated within the warranty period.
In no event will MJ Research, Incorporated be responsible for damage resulting from accident,
abuse, misuses, or inadequate packaging of returned goods.
Any implied warranties, including implied warranties of the merchantability and fitness for a
particular purpose, are limited in duration to two years from the date of original retail purchase of
this product.
The warranty and remedies set forth above are exclusive and in lieu of all others, oral or written,
expressed or implied. No MJ Research dealer, agent, or employee is authorized to make any modi-
fication, addition, or extension to this warranty, except in the form of the extended warranty out-
lined below.
MJ Research, Incorporated is not responsible for special, incidental, or consequential damages
resulting from any breach of warranty, or under any other legal theory, including downtime, lost
samples or experiments, lost reagents, lost profits, goodwill, damage to or replacement of equip-
ment, property, and any costs of recovering or reproducing experimental results and data.
Exclusions: This warranty applies only to machines sold in the U.S.A. and Canada. Under no circum-
stance will MJ Research, Incorporated ship a repaired or replaced machine, or grant a refund of pur-
chase price, to a user in a nation in which there was an authorized MJ Research distributor at the time
of purchase. This warranty is not transferable from the original purchaser to a subsequent owner.
Furthermore, this warranty does not apply to instruments used outside the U.S.A. and Canada, except
when expressly authorized in writing by MJ Research, Incorporated.
U.S. & Canadian Extended Warranty, Optional

MJ Research, Incorporated will offer to each original purchaser of an MJ Research brand thermal
cycler the opportunity to purchase an extension of the warranty coverage explained above for an
additional two years. The coverage must be purchased through a purchase order received by MJ
RESEARCH, INCOrporated within 30 days of receipt of the offer of extended warranty or the offer to
renew the extended warranty. These offers apply only to machines sold and used in the U.S.A.
and Canada.
D-1
Some states of the U.S.A. do not allow the exclusion or limitation of incidental or consequential
damages or limitations on how long an implied warranty lasts, so the above limitation or exclu-
sion may not apply to you. This warranty gives you specific legal rights. You may also have other
rights depending upon your state of residence.
All provisions of this warranty are voided if the product is resold, repaired, or modified by any-
one other than MJ Research, Incorporated or an authorized distributor.
D-2
Appendix E
Appendix E
Shipping Instructions for US

Residents
Users residing in the United States should follow these instructions for shipping a machine to MJ
RESEARCH for factory repair or an upgrade. Users outside of the United States should send ma-
chines to their distributor, in accordance with shipping instructions obtained from the distributor.
1. Call MJ RESEARCH to obtain a return materials authorization (RMA) number. Machines returned
without an RMA number will be refused by the Receiving Department.
2. Thoroughly clean the machine, removing excess oil and radioactive and other biohazardous
substances. To protect the health of our employees, MJ RESEARCH will not repair or upgrade
any machine that is excessively oily or that emits ionizing radiation upon arrival at our fac-
tory. PLEASE ELIMINATE ALL BIOHAZARDS!
3. Pack the machine in its original packaging. If this has been misplaced or discarded, call MJ
RESEARCH to request shipment of packaging materials. You can also request a loaner machine,
which will be provided if available (a rental fee may apply). You can use the loaner’s packag-
ing to return the machine needing repair.
4. Write the RMA number on the outside of the box.
5. Ship the machine (freight prepaid) to the following address. We recommend you purchase
insurance from your shipper.
Ship to: Repair Department
MJ Research, Incorporated
590 Lincoln Street
Waltham, MA 02451
E-1
Index
A F
Accessories. See Probe, Slide Griddle FCC warning, B-2
Air supply requirements. See Setting up the Fuses, changing, 8-2
machine
G
B GoTo step, 6-2
Block control. See Temperature control meth- entering, 6-6
ods
Blocks available. See Models available
H
Hot Bonnet, 4-6, 4-9, 4-10
C adjusting lid pressure, 4-7
Chart recorders, 5-8 beeping, 5-2
sources of, 5-8
Chill-out liquid wax, 4-5, 4-6
Cleaning
I
air vents, 8-2 Improving thermal contact. See Oil, using in
radioactive materials, 4-16, 8-2 block
biohazardous materials, 8-2 Increment step, 6-2
chassis and block, 4-16, 8-2 entering, 6-7
solutions to use, 4-16, 8-2 Instant incubations, running, 5-6
Condensation in tubes following holds, 4-7
Control panel
keys, 4-2
L
lights, 4-3 Layout
16MS Slide Block
front view, 2-6
D cold lid models
Documentation conventions, iv back view , 2-3
Declaration of Conformity, DoC-1 control panel, 2-3
front view, 2-2
Hot Bonnet models
E back view, 2-5
Electromagnetic interference statement, B-1 front view, 2-4
End step, 6-2 LED bar graph, reading, 5-3
entering, 6-10 Lid, opening and closing, 4-3
Error messages, 9-2
Extend step, 6-2
entering, 6-8
IN-1
MiniCycler Operations Manual
M entering steps
End step, 6-10
Manually stepping programs. See Program-
extend step, 6-8
ming, Protocols
GoTo step, 6-6
Menus
increment step, 6-7
Enter Menu, 6-5
slope step, 6-9
Main Menu, 6-4
temperature step, 6-5
Run-Enter Menu, 4-2
indefinite holds, 6-10
Microplates, 4-4
initiating a program, 6-4
polycarbonate, 4-4
Programs
polypropylene, 4-4
deleting from memory, 6-12
U-bottom PVC, 4-4
designing, 6-2
Microseal
choosing a temperature control method. See
'A', 4-7
Temperature control methods
'M', 4-7
translating a protocol into a program, 6-2
Models available
using GoTo steps to shorten a program, 6-2
16MS Slide Block, 2-2
editing, 7-2
cold lid, 2-2
changing temperatures or cycling values,
Hot Bonnet, 2-4
7-2
changing time values, 7-3
O getting into Edit mode, 7-2
slope steps, 7-4
Oil, using in block, 4-9
listing steps on screen, 6-12
amount to use, 4-9
naming, 6-5
disadvantages, 4-9
printing. See Printing
protecting against loss, 6-14
P types of steps, 6-2
Packing list, 3-2 Protocols
Power supply requirements. See Setting up manually stepping through, 5-4
the machine pausing while running, 5-4
Printing problems with, 9-3
log of running protocol, 5-6 protocol completion screen, reading, 5-4
programs, 6-13 reading LED bar graph while running, 5-3
temperature record for block, 5-8 reading runtime screen, 5-3
Probe, 4-10 resuming after power outage, 5-5
adding oil, 4-11 running, 5-2
calibration, 4-12 under probe control, 4-12, 5-2
connecting to machine, 4-12 stopping, 5-5
customizing, 4-10
description, 4-10 R
loading into block, 4-12
types of oil to use in, 4-11 Ramping speed, 6-10
Probe control. See Temperature control methods Runtime screen, reading, 5-3
Programming
creating a program that requires manual S
stepping, 6-10
deleting an incomplete program, 6-12 Safe use guidelines, B-1
editing while, 6-11 Safety warnings, 8-3, B-1
IN-2
Index
Sample vessels
loading into block, 4-8. See also 16MS Slide
Block
sealing, 4-5
16MS Slide Block, 4-5
with Hot Bonnet and caps/film, 4-6
with oil or wax, 4-5
selecting
0.2ml tubes, 4-3
0.5ml tubes, 4-3
microplates, 4-4
thin-walled vs. thick-walled tubes, 4-5
Self-test, 4-2
Setting up the machine, 3-2
air supply requirements, 3-3
environmental requirements, 3-2
power supply requirements, 3-3
Shipping instructions, D-1
16MS Slide Block
cleaning, A-3
description, A-1
loading sample vessels into block, A-2
preparing and sealing sample vessels, A-1
programming, A-2
selecting sample vessels, A-1
Slide Griddle, 4-10
Slope step, 6-2
entering, 6-9
Specifications, 2-8
Sponge rubber pad, 4-9
T
Temperature control methods
block control, 6-3
probe control, 4-10, 6-3
Temperature step, 6-2
entering, 6-5
Thin-walled tubes, advantages of. See Sample
vessels: Thin-walled vs. thick-walled
tubes
Troubleshooting
error messages, 9-2
problems with machine performance, 9-5
problems with protocols, 9-3
Turning the machine on, 4-2
IN-3
Declaration of Conformity
DoC-1

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PTC-100 Operations Manual

In the United States: In other nations:

Documentation Conventions ............................................................................................... iv

1. Introduction ................................................................................................................. 1-1

Appendix A: The 16MS Slide Block ................................................................................ A-1

Index ..................................................................................................................................... In-1

Declaration of Conformity ............................................................................................... DoC-1

Items in programming menus are italicized:

Example: Select Edit from the Main Menu.

Example: RUN Enter

Meet the PTC-100 ......................................... 1-2

How to Use This Manual .............................. 1-2

Important Safety Information ..................... 1-2

Meet the PTC-100

How to Use This Manual

Note: Information on installing, operating, and programming the 16MS

Important Safety Information

PTC-100 with Cold Lid .................................. 2-2

PTC-100 with Hot Bonnet ............................. 2-4

PTC-100 with 16MS Slide Block (Fig. 2-6) ...... 2-6

Accessories ................................................. 2-7

Specifications .............................................. 2-8

PTC-100 with Cold Lid

Front View (Fig. 2-1)

Air exhaust vents

Air intake vents

Back View (Fig. 2-2)

Chart recorder jack

Hot Bonnet jack (unused

Control Panel (Fig. 2-3)

LED bar graph

PTC-100 with Hot Bonnet

Front View (Fig. 2-4)

Lid release button

Air exhaust vents

Air intake vents

Back View (Fig. 2-5)

Chart recorder jack

Hot Bonnet jack (with

Air intake vents

PTC-100 with 16MS Slide Block

Air exhaust vents

Air intake vents

Probe tube, with sensor inside

Slide Griddle Adapter (Fig. 2-8)

Active slide griddle Passive slide griddle

Packing List ................................................. 3-2

Setting Up the PTC-100 ................................ 3-2

Environmental Requirements ....................... 3-2

Power Supply Requirements ....................... 3-3

Air Supply Requirements ............................. 3-3

Setting Up the PTC-100

Power Supply Requirements

Air Supply Requirements

Opening and Closing the Lid ........................ 4-3

Sealing Sample Vessels ............................... 4-5

Loading Sample Vessels .............................. 4-8

Using the Slide Griddle ................................ 4-10

Turning the PTC-100 On