PCR Express User Manual

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THERMO HYBAID

PCR Express Thermal Cycler

USER INSTRUCTION MANUAL

Head Office

Thermo Hybaid

Action Court

Ashford Road

Ashford

Middlesex TW15 1XB

Telephone: +44 (0) 1784 425000

Free Phone UK: 0500 95 55 72

Facsimile: +44 (0) 1784 248085

STOCK CODE:

HB-PX-MAN

FS31999

PCR EXPRESS TEMPERATURE CYCLING SYSTEM

PCR License Registration

This instrument, Serial No. ................................................ is an Authorized Thermal Cycler.

Its purchase price includes the up-front fee component of a license under the patents on the

Polymerase Chain Reaction (PCR) process, which are owned by Hoffmann-La Roche Inc. and

F. Hoffmann-La Roche Ltd, to practise the PCR process for internal research and development

using this instrument. The running royalty component of that license may be purchased from

Perkin-Elmer or obtained by purchasing Authorized Reagents. This instrument is also an

Authorized Thermal Cycler for use with applications’ licenses available from Perkin-Elmer.

Its use with Authorized Reagents also provides a limited PCR license in accordance with the

label rights accompanying such reagents. Purchase of this product does not itself convey to

the purchaser a complete license or right to perform the PCR process. Further information on

purchasing licenses to practice the PCR process may be obtained by contacting the Director of

Licensing at The Perkin-Elmer Corporation, 850 Lincoln Centre Drive, Foster City, California

94404, USA. Tel No: + 415 638 5551. Fax No: +415 638 6071.

Perkin-Elmer does not guarantee the performance of this instrument.

PCR EXPRESS TEMPERATURE CYCLING SYSTEM

Warranty

Thermo Hybaid guarantees that the PCR Express Temperature Cycling system you have

received has been thoroughly tested and meets its published specification.

This guarantee is valid for 36 months only if the product and functions have been used

according to the instruction manual. No liability is accepted for loss or damage arising from

the incorrect use of the PCR Express Temperature Cycling system. Thermo Hybaid's liability

is limited to the repair or replacement of the unit or refund of the purchase price at Thermo

Hybaid's option. Thermo Hybaid is not liable for any consequential damages.

The tube thermistor assembly supplied with your PCR Express unit is guaranteed for 90 days.

Thermo Hybaid reserves the right to alter the specification of the PCR Express without prior

notice. This will enable us to implement developments as soon as they arise.

The Thermo Hybaid PCR Express is for research use only.

Read the Instruction Manual carefully before using the PCR Express to ensure that you

obtain the best possible results from the machine.

NB: The PCR Express should only be used by suitably qualified and trained people. If

the PCR Express is not used as specified in this Manual, the protection provided by

the equipment may be impaired.

PCR EXPRESS TEMPERATURE CYCLING SYSTEM

Contents

PCR LICENSE REGISTRATION ..................................................................................... iii

WARRANTY ........................................................................................................................ iv

CHAPTER 1: INTRODUCTION ......................................................................................1

1.1 Overview ............................................................................................1

1.2 PCR Express System.........................................................................1

The 0.2ml Block Module & 0.2ml Gradient Block Module...............1

The 0.5ml Block Module & 0.5ml Gradient Block Module...............2

The Flat Block Module .......................................................................2

The 384 Well Block Module ..............................................................2

Temperature Control Methods............................................................2

Heating and Cooling ...........................................................................3

Programming and Operation...............................................................3

Pre-set Programs .................................................................................3

Advanced Edit.....................................................................................4

Temperature Control...........................................................................4

1.3 The Heated Lid..................................................................................4

1.4 Support Services................................................................................6

CHAPTER 2: SAFETY PRECAUTIONS ........................................................................7

Symbols and Conventions ............................................................................8

CHAPTER 3: UNPACKING & INSTALLATION .........................................................9

3.1 Unpacking..........................................................................................9

3.2 Packing List .......................................................................................9

3.3 Installation.......................................................................................10

Block Installation and Removal........................................................10

Thermistor Positioning......................................................................10

Choosing a Location .........................................................................11

Use in Cold Rooms ...........................................................................11

CHAPTER 4: OPERATING INSTRUCTIONS ............................................................13

4.1 Initial Start Up ................................................................................13

4.2 Main Menu ......................................................................................13

4.3 Operating Keys................................................................................14

4.4 Set Up Functions .............................................................................14

Clock.................................................................................................14

Power Failure Resume ......................................................................15

Display Adjustment...........................................................................15

4.5 Running a Program ........................................................................15

4.6 Manual Operation...........................................................................15

4.7 Programming Function ..................................................................18

4.8 Loading Samples and Heated Lid Operation......................... 18/19

Set Switch .........................................................................................19

CHAPTER 5: PROGRAMMING THE PCR EXPRESS ..............................................21

5.1 Introduction.....................................................................................21

5.2 Directories........................................................................................21

5.3 Steps and Stages of a Program ......................................................22

5.4 Creating a New Program................................................................22

5.5 Editing an Existing Program .........................................................26

5.6 Viewing an Existing Program ........................................................29

5.7 Copying Programs ..........................................................................29

5.8 Erasing a Program..........................................................................29

5.9 Advanced Edit Features .................................................................30

Time Advanced Edit Worked Example ............................................30

Temperature Advanced Edit Worked Example ................................32

Changing Ramp Rates.......................................................................33

5.10 Gradient Feature.............................................................................34

Gradient Programming Worked Example.........................................35

Gradient Calculator Function............................................................36

CHAPTER 6: RUNNING A PROGRAM ON THE PCR EXPRESS ..........................39

6.1 The RUN Option .............................................................................39

6.2 Running A Program on the PCR Express ....................................39

6.3 Example Run Screens .....................................................................41

6.4 Temperature Control Options .......................................................43

Active Tube Control .........................................................................43

Simulated Tube Control....................................................................44

Simulated Plate Control ....................................................................45

Simulated Slide Control....................................................................47

Block Control....................................................................................47

6.5 Heated Lid Preheat .........................................................................47

Heated Lid - Automatic Start............................................................47

Heated Lid - Manual Start.................................................................48

No Heated Lid...................................................................................48

6.6 Hold and Pause Function ...............................................................48

6.7 Aborting Programs .........................................................................49

6.8 Program Completion ......................................................................49

CHAPTER 7: TROUBLESHOOTING...........................................................................51

7.1 Protocol transfer .............................................................................53

CHAPTER 8: MAINTENANCE .....................................................................................57

8.1 General Cleaning ............................................................................57

8.2 Decontamination .............................................................................57

8.3 Protection to the User .....................................................................58

8.4 Protection of the Instrument..........................................................58

Fuses .................................................................................................58

8.5 Tube Thermistor Care....................................................................58

viii

CHAPTER 9: TECHNICAL SPECIFICATIONS &

ORDERING INFORMATION ...............................................................61

9.1 Consumables....................................................................................66

APPENDIX I: SOFTWARE UPGRADE VIA RS232 ....................................................67

APPENDIX II: SEALING SYSTEMS: THE OMNISEAL TD MAT & TD TAPE .....69

APPENDIX III: IN SITU BLOCK APPLICATION NOTES ..........................................73

APPENDIX IV: COMPARATIVE PERFOERMANCE DATA

(AMBIENT & SUB AMBIENT SYSTEMS) .........................................75

APPENDIX V: GLOSSARY OF TERMS ........................................................................77

APPENDIX VI: PRE-SET PROGRAMS ON THE PCR EXPRESS ..............................81

CHAPTER 1

PCR EXPRESS THERMAL CYCLER

Introduction

1.1 Overview

PCR Express is the essence of fast accurate, licensed thermal cycling. PCR Express features

high capacity, high speed and sub-ambient blocks to perform oil-free thermal cycling with

excellent dynamic uniformity and precision control of sample temperature.

1.2 PCR Express System

The PCR Express System comprises a Control Chassis and an Interchangeable Block Module.

Each control chassis can operate one block module, which can be changed according to the

needs of the sample format. There are six types of block module:

The 0.2ml Block Module & 0.2ml Gradient Block Module

This block can hold any of the following:

• 1 x OmniPlate 96 well plate

• 1 x OmniTube 96 single piece polypropylene plate

• 96 x 0.2ml OmniStrip tubes

• 96 x 0.2ml individual OmniTubes

The 0.5ml Block Module & 0.5ml Gradient Block Module

This block can hold any of the following:

• 1 x 96 well plate (e.g. Costar Thermowell H)

• 96 x 0.3ml OmniStrip tubes

• 96 racked 0.3ml OmniTubes

• 48 standard 0.5ml individual OmniTubes.

The Flat Block Module

This block accommodates up to four standard microscope slides.

The 384 Well Block Module

This block accommodates 1 x OmniPlate 384 polypropylene plate.

Temperature Control Methods

The temperature cycling blocks for the system are of a specially coated precision-machined

aluminium, ensuring the best possible fit of reaction tubes in the block. This ensures excellent

contact between the tubes and the block, enabling rapid and accurate heat transfer from the

block to the samples.

1. Active Tube Control

Accurate sample temperature control in 0.2ml and 0.5ml block types is achieved by Thermo

Hybaid's Active Tube Control software. The tube thermistor probe monitors the temperature

within a dummy sample tube and this information is fed back to precisely control the block

temperature to achieve the optimum cycling profile.

2. Simulated Tube/Plate Control

Alternatively, Simulated Tube Control or Simulated Plate Control may be used for

reactions when it is not appropriate to use the tube thermistor probe, for example in very small

(<20µl) reactions or reactions in 96 Well or 384 Well OmniPlates or racked OmniTubes. The

temperature control algorithm is similar to active tube control, but is based on calculated

values for the sample temperature rather than values fed back by the tube thermistor.

3. Simulated Slide Control

For the In Situ module Simulated Slide Control should be selected. This operates on a

similar principle to Simulated Tube Control, but in this case the algorithm is based on

achieving the set temperatures at the top surface of a standard glass microscope slide (1mm

thick).

Heating and Cooling

The PCR Express sub-ambient blocks are built to proven designs, providing an accurate and

reliable thermal cycling system.

The sub-ambient aluminium block is heated and cooled by the latest in Peltier technology.

With proven durability, the block modules excel in performing applications such as RAPD

and Differential Display, which require cycling temperatures close to ambient. The block

modules will control the temperature of the samples from 20°C to 99°C for cycling reactions

in all reaction formats. In addition, static incubation steps may be performed as low as 4°C.

Programming and Operation

Cycling programs are simple to perform, using the combination of user-friendly screens and

operating keys. During programmed operation, the display screens provide comprehensive

information for the block including sample temperature, number of cycles completed,

estimated time for completion, etc.

The PCR Express can thus be programmed to perform all types of temperature controlled

reactions, from simple one step incubations, to complex multi-step temperature cycling

protocols and temperature gradient experiments*. Three additional temperature control

software options are available to the user in the Advanced Edit Menu: Temperature Ramping,

Time Increment and Temperature Increment.

The unit has program space for up to 99 full cycling protocols including the pre-set protocols.

* With the gradient interchangeable block options.

Pre-set Programs

The PCR Express is supplied with ten non-editable pre-set protocols stored as programs 90-99

in the F:HYBAID directory. These cover the most common thermal cycling techniques, and

can be used to create customised protocols by editing (see Appendix VI).

Advanced Edit - Temperature Ramping

The temperature ramping (Ramp Rate) enables the rate of change of sample temperature

(°C/second) to be artificially slowed down.

Under normal circumstances the temperature cycling times are very rapid, which minimises

non-specific reactions. The rate of sample temperature change during temperature cycling is

controlled so that it is as fast as possible without affecting the block uniformity and accuracy.

In some instances, it may be advantageous to limit the rate of change of temperature, e.g. to

allow limited extension of short or degenerate primers between primer annealing and DNA

synthesis steps to stabilise the primer/template duplex.

Advanced Edit - Time/Temperature Increment

These features enable the time interval and/or the temperature of a specified programmed step

to be increased or decreased with successive temperature cycles. It may be advantageous to

increment the extension time interval to compensate for deterioration of enzyme activity in

later cycles. Alternatively, temperature decrements can be used, e.g. in PCR Express cycling

reactions where the annealing temperature is decreased with successive cycles.

Temperature Control

Every machine is calibrated using miniature thermistor probes located in tubes or attached to

microscope slides. These are placed at several block positions simultaneously, ensuring the

required temperatures and incubation times achieved are identical in all samples.

1.3 The Heated Lid

The unique auto-adjust Heated Lid enables the running of temperature cycling protocols

without the need for paraffin or mineral oil overlays. Such vapour barriers are normally

required to prevent evaporation before thermal cycling is complete. This system is designed to

be compatible with most reaction sample formats, i.e. 0.5ml, 0.3ml, 0.2ml tubes and 96/384

well plates. In most cases, the experimental protocol is largely unchanged when switching to

an oil free format.

The Heated Lid operates by positioning a heated plate in contact with the top of the reaction

tubes or wells. This heated plate then heats the air temperature at the top of each reaction

mixture to a temperature that is permanently higher than the sample temperature. This

elevated air temperature, relative to the sample temperature, minimises evaporation so that

there is no condensation of the reaction mixture as it is repeatedly heated and cooled.

Opening the Lid

The lid is opened by lifting the light blue catch, and pushing it back.

The mechanism operates in 2 stages but through one continuous action; the first part of the

action raises the heating plate within the machine, the second releases the catches at the front

of the unit to raise the lid and expose the block recess.

Closing the Lid

To close, gently lower the dark blue lid and depress the light blue catch. At this point a ‘click’

should be heard as the catches are engaged. This action lowers the heated lid on to the

samples and closes the unit, ensuring tight contact.

The height of the heating plate inside the Heated Lid is automatically adjusted as the lid is

closed. The downward pressure can be adjusted using the set switch according to whether

light pressure (300g for tubes) or greater force (3.5kg to maintain the seal on plates) is

required.

The temperature of the heating plate is set at 115°C (max. surface temperature) with power

control effected by the control chassis.

The heated plate inside the lid is switched on and off from within the program. The lid

operates once a program is activated, with a heating time of typically 2 minutes before cycling

commences. The unit can be operated with or without the lid being switched on (the lid is

automatically deactivated in units fitted with flat block modules).

1.4 Support Services

The PCR Express has been designed for reliability and for ease of maintenance. Thermo

Hybaid continues to offer full service and technical support for all its products.

Telephone Contacts:

International Sales, Service and Technical Support (UK) +44 (0)1784 425000

UK Sales and Technical Support 01784 425000/(Freephone) 0500 95 55

UK Service Support 01784 425000/(Freephone) 0500 49 22

Fax Contacts:

UK & International Sales, Service & Technical Support (UK) +44 (0) 1784 248085

Alternatively, contact your local Thermo Hybaid subsidiary or authorised distributor.

CHAPTER 2

PCR EXPRESS THERMAL CYCLER

Safety Precautions

General Safety Precautions

1. The PCR Express should only be used by suitably qualified and trained personnel. The

unit should only be used for its intended purpose in accordance with the instructions and

safety warnings contained within this manual.

2. Before use, ensure that the unit has been set to the appropriate mains voltage.

3. The PCR Express is a class 1 appliance. To minimize the risk of electric shock, the unit

must be connected to a protective earth via the supplied mains cord.

4. Replacement fuses must be of the correct rated current, voltage and type.

5. Do not operate the unit in an explosive environment.

6. Do not operate the unit if it appears to be damaged or if a liquid or foreign object has

entered the enclosure. Disconnect from the mains supply and contact an authorized

service centre.

7. Do not attempt to dismantle the unit. To avoid the risk of personal injury and to ensure

that the safety features of this unit are maintained, servicing should only be carried out by

authorized service personnel.

8. The tops of the reaction vessels and the surfaces of the Heated Lid assembly (in particular

the inner surfaces) can become very hot during normal operation. Touching the surfaces

can cause burns. Do not touch the heated plate without safety gloves.

9. When positioning the unit ensure that there is no restriction to the power inlet. Special

care should be taken not to obstruct the vent underneath the unit, for example loose

Benchcote or sheets of paper.

10. When installing/removing the interchangeable block

• Ensure that the power to the instrument is turned off.

• The Block Heat Sink may be hot after use. Use gloves when interchanging

blocks if the unit has been used recently.

11. This product is fitted with RFI suppression circuitry. Testing of the electrical insulation

should only be carried out using a DC voltage. For more information please contact

Thermo Hybaid.

Symbols & Conventions

The PCR Express has been designed for safe operation. The following symbols appearing on

the unit and their meanings should be noted.

IIndicates the ON position of the main power switch.

OIndicates the OFF position of the main power switch.

Consult the manual for further information.

Consulter les documents d’accompagnement.

WARNING: Indicates a heating hazard. Proceed with caution to avoid burn

injury.

ATTENTION: Surface chaude.

SAFETY NOTE: This symbol indicates high voltage. Risk of electric shock.

AVERTISSEMENT: Risqué de choc éléctrique.

In addition, the following conventions are adopted in the manual in respect of indicating safety

hazard:

SAFETY NOTE: indicates a potentially hazardous situation, which could result

in death or serious injury.

WARNING: indicates a potentially hazardous situation, which could result in

minor or moderate injury to the user or damage to the instrument.

CHAPTER 3

PCR EXPRESS THERMAL CYCLER

Unpacking & Installation

3.1 Unpacking

Before unpacking the PCR Express, please make sure that the outer packaging is undamaged.

After unpacking, ensure all packaging and fixtures are retained, as the unit should always be

transported in the original packing to avoid damage. Thermo Hybaid cannot accept

responsibility for any damage incurred if the unit is incorrectly packed and transported.

3.2 Packing List

1. PCR Express Control Chassis

2. PCR Express Block Module

3. User Instruction Manual

4. Mains Lead

5. Control Thermistor Probe (0.2ml and 0.5ml gradient and standard block modules)

6. Control Thermistor Probe Extension Lead (0.2ml and 0.5ml gradient and standard block

modules)

7. Specific Consumable Pack

8. RS232 Lead

9. Self Adhesive Unit Identity Label

NB: The In Situ Flat Block Module includes a humidity chamber.

If any item is missing or damaged, contact the UK Service Department, or your local Thermo

Hybaid office/authorised distributor.

Ensure any padding between the plate inside the Heated Lid and the block is removed before

using the instrument.

3.3 Installation

Block Installation and Removal

1. Remove the PCR Express Control Chassis and Block Module from the packaging and

place on the bench; do not connect to the mains supply immediately.

2. Open the lid (by lifting the light blue latch) to expose the block recess.

3. Supporting the block from the blue plastic moulding and the ring pull, position the back

of the block on the two lugs on the chassis.

4. Lower the block, via the pull ring into the recess (see fig 3.1). Placing your thumb on

the ring pull (just beneath the hole) firmly push downwards until you hear the block

click into place.

5. Do not force the block if this does not happen: remove the block and check for

obstructions in the block recess. The following error screens will appear if the block has

not been installed properly or you attempt to run a program without a block in place:

SELF CHECK FAILED or SELF CHECK FAILED

BLOCK NOT PRESENT BLOCK ID ERROR

Removal is the reverse procedure.

Figure 3.1 Installing the Block Module

Thermistor Positioning

The control thermistor probe (when required) should be inserted into socket A2 to the left of

the block towards the rear of the instrument (see fig 3.2).

Ensure that the tube contains the same volume of mineral oil as the sample reaction volume,

and that the probe is immersed in the oil.

Figure 3.2 Well Numbering Showing Tube Thermistor Positioning in A2

Choosing a Location

1. Where possible, avoid connecting the Control Chassis to a mains supply subject to mains

voltage fluctuations, e.g. a socket shared by an ultracentrifuge or refrigerator.

2. In PCR Express systems, excess heat is removed from the system by a fan. Therefore,

allow at least 8cm clearance between the sides of each module and any restriction to the

flow of air. Allow 15cm of clearance at the back of the unit. The air intake is located

underneath and air is expelled out of the back of the unit. Care should be taken not to

obstruct the vent underneath the unit with, for example, loose Benchcote or sheets of

paper. The unit must not be covered during operation.

3. All PCR Express instruments should be placed on a stable and level surface, out of direct

sunlight and away from strong currents of hot or cold air. The heated lid should always be

closed during temperature cycling, even if the lid is not switched on.

4. The PCR Express is intended for indoor use at an ambient temperature of 4-34°C in

conditions of up to 80% humidity. These specifications have been calculated for

operations at between 0 and 2000m altitudes.

Use in Cold Rooms

The PCR Express may be used in a cold room (down to 4°C). However, when removed to

room temperature the instrument should be allowed to equilibrate for at least two hours before

being switched on. If equilibration is not done, condensation may form within the unit and

cause a short circuit.

112

CHAPTER 4

PCR EXPRESS THERMAL CYCLER

Operating Instructions

4.1 Initial Start Up

(a) Switch on the PCR Express at the power switch at the rear of the unit. When first

switched on the unit will complete a start up and self test routine.

(b) After 10 seconds a screen will display “PCR Express going through a self test

procedure”. This procedure need only be followed once a week. This can be by-passed

by pressing the CONTINUE key when the initialisation screen is visible.

heated lid. This takes approximately 2 minutes. (As the block will become hot during

the self-test procedure, please keep the lid closed.)

4.2 Main Menu

After successful start up, the first menu to be displayed is the ‘Main’ Menu. It is possible to

return to this menu at any time by pressing ‘MENU’. The Main Menu displays the date, time

and the status of the block (active, inactive, interrupted or active resumed).

All aspects of the programming are accessed through the Main Menu.

Table 4.1 Summary of Main Menu Functions

RUN Select RUN to run an existing program.

MAN Select MAN to run a manual static incubation.

PROG Select PROG to edit, copy, view or erase a program.

OPTS Select SET UP to alter the time, date, and power resume function and display

brightness settings and to identify software version fitted.

Select CALC to access the gradient calculator software (only relevant to gradient

protocols).

4.3 Operating Keys

The PCR Express software is designed to be intuitive, the following table gives a summary of

the primary functions of each of the operating keys.

KEY FUNCTION

ENTER KEY - Selecting Menu and program choices.

MENU KEY - Always moves to the Main Menu – (can be utilised as an “escape” key).

NUMBER KEYS - Used for entering parameters and selecting programs.

ARROW KEYS - Moving cursor between program positions.

- Alphanumeric naming of programs/directories.

- Used to toggle between options.

- Used for rapid scrolling through programs and for moving between run

screens.

STOP KEY - Cancels instructions/operations/programs.

- Used to delete programs & directories.

CONTINUE KEY - Used to progress from “hold”, “pause” or “self test” instructions.

- Also used to access advanced edit functions.

PAUSE KEY - Pauses a cycling program at current step.

BLOCK KEY - Provides access to current/historical information on block status

screens.

These functions are discussed fully in the following chapters.

4.4 Set Up Functions

Selecting SETUP at the Main Menu and pressing ENTER gives access to the SETUP menu.

The SETUP menu also displays the current software version.

Clock

The time and date format of the clock display can be modified. To set the clock or alter the

format, select CLOCK from the SETUP menu and press ENTER.

The American (MM/DD/YY) or European (DD/MM/YY) format can be selected using the Î

key.

Press ENTER to move to the time/date setting fields. Use the number keys to enter time (hrs

& mins) and day/month/year information. Press ENTER to return to the Main Menu.

Power Failure Resume

If there is a power interruption during a run, the PCR Express will switch back on

automatically. The unit can be set to resume a program (at the cycle and setpoint where the

interruption occurred) or to abandon the program. Select POWER from the SETUP menu and

press ENTER. The ABANDON or RESUME options can be selected using the Î key.

Press ENTER to return to the Main Menu.

The instrument will record the duration of the interruption and the step, stage and cycle

number at which it occurred.

(Note that if there have been several breaks in the power supply, only the most recent

interruption is recorded.)

Display Adjustment

The display brightness can be adjusted under varying light conditions.

• Select DISPLAY from the SETUP menu, and press ENTER.

• Hold down Ï or Ð to increase or decrease the brightness observed on the screen.

• Press ENTER to save the current screen brightness and return to the Main Menu.

4.5 Running a Program

Running a pre-stored program is easy on the PCR Express.

• At the Main Menu, with the cursor on RUN, press ENTER.

• Select the source directory (e.g. F:HYBAID) and press ENTER then select program

number to be run and follow the screen prompts.

Prior to starting the program, pressing the MENU key at any stage, will return to the Main

Menu. More details can be found in Chapter 6.

4.6 Manual Operation

This option is used for static incubations when thermal cycling is not required, e.g. hot start

protocols, probe denaturations, enzyme reactions. In this mode the unit will operate under

block control (see Chapter 5 for details). The count-up timer will start when the block reaches

temperature.

1. Select MAN from the Main Menu and press ENTER.

2. Enter the name of the user or protocol if desired using the Ï and Ð arrows to scroll

through the characters. Move to the next/previous character using the Í and Î arrow

keys.

3. Enter the temperature using the numeric keys. Press ENTER to continue.

4. Select the heated lid on (auto) or off using the Î key.

5. Press ENTER to start the incubation. The screen displays the set temperature and actual

temperature of the block together with the elapsed time.

NB: If the machine is started from ‘cold’, approximately two minutes will be required

before the Heated Lid is at operating temperature (based on 20°C ambient and

230V supply. This may vary under different power conditions). Condensation may

be experienced if samples are loaded before the lid is at operating temperature.

6. Press STOP twice to cancel the manual program.

7. Press CONTINUE to change the set temperature.

(See Figure 4.1 on the following page)

Figure 4.1:Using the PCR Express for static temperature incubations (Manual control)

2 0 / 0 7 / 9 9 1 2 : 0 1 : 0 0

I N A C T I V E

M A I N M E N U

R U N M A N P R O G O P T S

(1) Press ENTER to select the MANUAL mode.

↓

↓↓

↓

M A N U A L U S E R H Y B A I D

T E M P 3 7 . 0

H O T L I D O F F

< E N T E R > T O C O N T I N U E

(2) Use Ï,Ð,Î, and Í to enter name then press ENTER.

↓

↓↓

↓

M A N U A L U S E R H Y B A I D

T E M P 4 5 . 0

H O T L I D O F F

< E N T E R > T O C O N T I N U E

(3) Use number keys to enter the required temperature, then press ENTER.

↓

↓↓

↓

M A N U A L U S E R H Y B A I D

T E M P 4 5 . 0

H O T L I D O F F

< E N T E R > T O C O N T I N U E

(4) Use Î to toggle heated lid on (auto) or off, then press ENTER.

↓

↓↓

↓

M A N U A L U S E R H Y B A I D

T E M P 4 5 . 0 T I M E 0 5 : 0 0

B L O C K 4 5 . 0

< C O N T I N U E > N E W T E M P

(5) Press CONTINUE to change the setpoint temperature, or STOP to stop the

incubation

4.7 Programming Function

Programming PCR protocols of varying degrees of complexity can easily be created using

PCR Express. As with all operations of the PCR Express, programming is accessed from the

Main Menu. Press MENU to access the Main Menu screen.

Use the arrow keys to move the cursor to PROG, and then press ENTER to access the

Program Menu. If at any time you wish to stop programming, press MENU to return to the

Main Menu. Four options are available for programming:

1. EDIT: To alter the details of an EXISTING program or to create a completely NEW

program.

Note that if NEW is used, it will automatically move to the next available program

number.

2. COPY: Use the screen prompts to copy between programs stored on the PCR Express.

3. VIEW: To check the details of a previously stored program.

4. ERASE: To erase the details of a program, setting the parameters to zero.

These are discussed in detail in Chapter 5.

4.8 Loading Samples and Heated Lid Operation

The PCR Express will produce identical cycling profiles whether 1 or 96 samples are to be

analysed.

Loading Samples

The following guidelines maximise the uniformity and thermal transfer characteristics of the

block:

• Load samples uniformly across the block rather than in clusters. Spreading the thermal

load in this way maintains uniformity.

• If small numbers of samples are to be run, use dummy tubes to ensure that there is at least

one tube in each quadrant of the block. This facilitates even heated lid pressure for good

thermal transfer to the tubes.

• Care should be taken when matching block, consumable, control mode and sample number

(as shown below).

• Ensure tube caps are properly closed before loading the block.

Table 4.2 Consumable Compatibility Table

Type* Control Method** Block

0.5ml

Block

0.2ml

Notes

0.5ml TUBE

SIM TUBE 9X

Max. 48 tubes/block arranged in a

diagonal pattern e.g. A2, B1, A4, B3, C2,

D1 etc. (see also figure 3.2). Space out

tubes for even loading.

0.3ml TUBE

SIM TUBE

9X Max. 96 tubes/block.

Space out strips for even loading.

0.2ml TUBE

SIM TUBE (including

OmniTube 96, 96 well

arrays)

X9Max. 96 tubes/block

Space out strips for even loading.

OmniPlate

SIM PLATE ? 9Seal using TD Tape/compression pad or

OmniSeal mat for oil free operation (see

also App II). Use on 0.5ml blocks may

require optimisation**

U-Well

0.5ml

Plates

SIM PLATE 9X Sealing may be problematic for oil free

operation TD Tape is the best option.

* Details of Thermo Hybaid’s own consumable range are given in Chapter 9

** See Section 5.2

Heated Lid Operation

The Auto Adjust Heated Lid is simple to operate. In one action, the lid is closed and the

heated plate lowered to its correct height and pressure setting.

No adjustment is necessary to compensate for different height consumables.

Set Switch

The Set Switch allows selection between a higher and a lower pressure setting. The switch is

labelled “PLATE” and “TUBE”.

• “PLATE” setting should be used when sealing 96/384 well plates with TD

Tape/compression pad or OmniSeal TD Mats.

• “TUBE” setting should be used for all other consumables.

CHAPTER 5

PCR EXPRESS THERMAL CYCLER

Programming the PCR Express

5.1 Introduction

The design of the PCR Express is such that programming it is easy. The memory will hold up

to 99 complete thermal cycling protocols including 10 pre-programmed template programs

(Nos. 90-99 detailed in Appendix VI). Programs are identified by a number (01-99) and a

user defined name (up to 7 characters). Each program protocol type may then assign to a

directory, enabling you to group programs by user name.

To enter a new program you simply

i) Create a new directory

ii) Name a program

iii) Enter protocol parameters

iv) Save the program

5.2 Directories

There are five directories A-E which can be individually named. The sixth directory, F is

reserved for pre-set programs.

Directories can also be erased and renamed as required.

Once assigned to a directory, a program can be copied to another program space in either

the same or a different directory.

Creating a New Directory

1. From the Main Menu select PROG and ENTER

2. Select EDIT and ENTER

3. Select NEW and ENTER

4. Select NEWDIR and ENTER

5. Select the desired target directory (A-E) using the cursor keys and then ENTER.

6. You are now able to name the directory, using the Ï and Ð arrows to scroll through the

characters or the alphanumeric keypad. Move to the next/previous character using the

Î and Í arrow keys. Press ENTER only when the name is complete. If no characters

are entered, the default NO NAME will be entered.

5.3 Steps & Stages of a Program

The programs in the PCR Express are divided into ‘stages’ and ‘steps’ when displayed on

the screen. In a simple PCR program, a stage typically includes three steps where each step

refers to the temperatures and times within the protocol. E.g. Step 1: 95°C for 30 seconds,

Step 2: 55°C for 30 seconds, Step 3: 72°C for 30 seconds. In addition each stage can be

repeated for up to 99 cycles, and a ‘hold’ added to the end of the stage.

The PCR Express allows you to program up to 10 separate stages each with up to 10

separate steps. This means that even the most complex thermal cycling protocol may be

saved in a single program space.

5.4 Creating a New Program

Using the NEW Program Option

Figure 5.1

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

M A I N M E N U

R U N M A N P R O G O P T S

(1) Move cursor to PROG, then press ENTER to select.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

P R O G R A M M E N U

E D I T C O P Y V I E W E R A S E

(2) Move cursor to EDIT, COPY, VIEW or ERASE as required (in this case EDIT), then press

ENTER to select.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 9

I N A C T I V E

P R O G R A M E D I T I N G M E N U

E X I S T I N G N E W

(3) Move the cursor NEW program then press ENTER to select.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 9

I N A C T I V E

N E W M E N U

N E W P R O G N E W D I R

(4) Move the cursor to NEWPROG and press ENTER to select.

↓

↓↓

↓

S E L E C T D I R E C T O R Y :

A : A N I T A D : T H O M A S

B : A L I S O N E : D I A N A

C : D A V E F : H Y B A I D

(5) Move the cursor to desired target directory and press ENTER to select.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 1 S T E P 0 1

T E M P 0 0 : 0

T I M E 0 : 0 0 : 0 0

(6) The instrument allocates a program number of the next available program space. You are

now able to enter the name of the user or protocol, using the Ï and Ð arrows to scroll

through the characters or the alphanumeric keypad. Move to the next/previous character

using the Î and Í arrow keys. Press ENTER only when the name is complete. If no

characters are entered, the default NO NAME will be entered.

Note: If there are no free program spaces the PCR Express will prompt you to overwrite

an existing program.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 1 S T E P 0 1

T E M P 9 5 :0

T I M E 0 : 0 5 :0 0

(7) Enter temperature (e.g. 95oC) and time (hr:min:sec), as required. Use Î to move across

menu, or Ð to advance to the next step. The ENTER key can also be used to move to

the next step of the protocol.

Note: The arrow keys can be used to scroll backward or forward to correct a mistake.

The program will not allow you to advance to step 2 until a valid temperature and time

have been entered.

Continue to enter the remaining times and temperatures of this stage. If none are

required at the stage of the protocol, press ENTER (leaving each parameter at 0:0) until

you access the number of cycle’s screen.

N E W A : 0 5 P C R 6 0 C

S T A G E N U M B E R 0 1

N U M B E R O F C Y C L E S 0 1

H O L D T E M P 0 0 . 0

(8) Enter the number cycles for this stage using the alphanumeric keys. A hold step can

also be programmed after each stage. This is particularly useful for ‘hot start’ protocols.

If a hold step is not required, press ENTER to reach the next stage.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 2 S T E P 0 2

T E M P 9 5 :0

T I M E 0 : 0 0 :3 0

(9) Continue adding steps as required for stage 1 (max. 10 steps per stage).

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 1 S T E P 0 2

T E M P 6 0 :0

T I M E 0 : 0 0 : 3 0

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 1 S T E P 0 2

T E M P 7 2 :0

T I M E 0 : 0 0 : 3 0

(10) Press ENTER (or Ð key) with each parameter at zero to finish the last stage of your

protocol.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E N U M B E R 0 1

N U M B E R O F C Y C L E S 3 0

H O L D T E M P 0 0 . 0

(11) Enter the number of cycles. Enter a hold temperature if required. Press ENTER to go

to the next stage.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E 0 3 S T E P 0 1

T E M P 7 2 : 0

T I M E 0 : 0 5 : 0 0

(12) Enter any additional stages and steps you require up to a maximum of 10. Press

ENTER.

↓

↓↓

↓

N E W A : 0 5 P C R 6 0 C

S T A G E N U M B E R 0 2

N U M B E R O F C Y C L E S 0 1

H O L D T E M P 0 0 . 0

(13) Enter the number of cycles. Enter a hold temperature if required. If a hold temperature

is not entered the instrument will cool to room temperature once the protocol is finished.

Press ENTER to access the SAVE screen.

↓

↓↓

↓

S A V E A : 0 5 P C R 6 0 C

<E N T E R > T O S A V E

< M E N U > T O A B A N D O N

(14) Press ENTER to save the program.

5.5 Editing an Existing Program

When editing a program and saving as a different program, the COPY function should first be

used to save the program to a different program space (see Section 5.7) and then the copy

should be edited.

The program name can be edited or deleted at this stage although it will be saved unchanged if

the enter key is pressed without changing the data.

Advanced editing features (adjusting ramp speeds, changing time/temperature with successive

cycles) can be accessed by pressing the CONTINUE key at the relevant step. (See section

5.9.)

It is possible to edit programs whilst the PCR Express is running a different protocol.

Figure 5.2 Editing an existing program

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

M A I N M E N U

R U N M A N P R O G O P T S

(1) To edit and overwrite existing programs select PROG from the Main Menu.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

P R O G R A M M E N U

E D I T C O P Y V I E W E R A S E

(2) Select EDIT from the Program Menu.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 9

I N A C T I V E

P R O G R A M E D I T I N G M E N U

E X I S T I N G N E W

(3) Select EXISTING from the Program Editing Menu.

↓

↓↓

↓

S E L E C T D I R E C T O R Y :

A : A N I T A D : T H O M A S

B : A L I S O N E : D I A N A

C : D A V E F : H Y B A I D

(4) Move the cursor to the source directory and press ENTER to select.

↓

↓↓

↓

E D I T A : 0 5 N O N A M E

< E N T E R > T O C O N T I N U E

(5) The keypad numbers or ÏÐ keys can be used to select the number of the program to be

edited.

↓

↓↓

↓

E D I T A : 0 5 P C R 6 0 C

S T A G E 0 1 S T E P 0 1

T E M P 9 5 :0

T I M E 0 : 0 5 :0 0

(6) Use the cursor keys to edit the program name. Press ENTER to proceed.

↓

↓↓

↓

E D I T I N G A : 0 5 P C R 5 5 C

S T A G E 0 1 S T E P 0 1

T E M P 9 4 : 0

T I M E 0 : 0 2 : 0 0

(7) Use →

→→

→ to move across the menu, and ↓

↓↓

↓ or ENTER to advance through the fields. Time

and temperature parameters can be altered using the numerical keys as required.

Note: To increase the number of steps in a stage, simply input values into the zero

time/temperature fields. To decrease the number of steps in a stage just input the new

data over existing time/temperature values.

↓

↓↓

↓

E D I T I N G A : 0 5 P C R 5 5 C

S T A G E 0 1 S T E P 0 2

T E M P 0 0 : 0

T I M E 0 : 0 0 : 0 0

(8) To complete editing stage 1, press ENTER with each parameter set at zero.

↓

↓↓

↓

E D I T I N G A : 0 5 P C R 5 5 C

S T A G E N U M B E R 0 1

N U M B E R O F C Y C L E S 0 1

H O L D T E M P 0 0 . 0

(9) Enter any changed cycle number or hold temperature values. Press ENTER to proceed

to the next stage.

↓

↓↓

↓

N E W A : 0 5 P C R 5 5 C

S T A G E 0 2 S T E P 0 1

T E M P 9 4 :0

T I M E 0 : 0 0 : 2 0

(10) Edit steps in further stages as required. Press ENTER with each parameter at zero to

access the save screen.

↓

↓↓

↓

S A V E A : 0 5 P C R 5 5 C

< E N T E R > T O S A V E

< M E N U > T O R E T A I N

O L D P R O G R A M

(11) Press ENTER to save changes.

5.6 Viewing an Existing Program

It is possible to view existing programs without altering the information contained within

them.

1. Select PROG from the Main Menu, VIEW from the program menu and (using the Í

and Î keys) enter the source directory.

2. Use the ENTER key and Ï and Ð arrows to move through the program, and

CONTINUE to enter and leave the Advanced Edit information.

3. The MENU key closes the view screen, and returns to the Main Menu.

5.7 Copying Programs

Copying programs is necessary in, for example, modifying the pre-set programs described in

Appendix VI. To do this select COPY from the Program Menu and press ENTER.

Enter the directory (using Í and Î to select) and number of the source program (or use Ï

and Ð to locate the source program) and press ENTER. Enter the directory and number of

the target program (or scroll using Ï and Ð) to locate a target program space. Press ENTER

to copy the program. Note that any existing program data in the target program space will be

overwritten.

5.8 Erasing a Program

Programs can be erased to vacate program space for future use.

From the Program Menu, select ERASE and press ENTER.

Enter the directory (using Í and Î to select) and number of the program to be erased (or

scroll using Ï and Ð) and press ENTER to erase the program. Confirm erasure of the

program by pressing STOP as prompted or MENU to keep the program.

5.9 Advanced Edit Features

The Advanced Edit features allow the creation of more complex cycling protocols in order to

enhance experimental data. It is possible to program:

• An incrementation or decrementation of both time and temperature on a cycle-by-cycle

basis.

• The rate at which the temperature changes between two given temperatures.

Advanced Edit features are accessed by pressing the CONTINUE key at the temperature step

at which the function is to take effect. If Advanced Edit data already exists for any step -

<ADV> is indicated on the screen.

Enter and change Advanced Edit parameters using the number, arrow and ENTER keys. The

Advanced Edit feature can also be accessed from the normal EDIT program menu options if

Advanced Edit parameters are to be added to an Existing program.

If desired, the Advanced Edit feature can be deleted for the current step. To do this, set all the

parameters back to zero. The <ADV> message will then not be shown in the

temperature/time set up screen, denoting that no Advanced Edit functions are operating.

Time Advanced Edit Worked Example

The user can specify the increment/decrement per cycle for each program stage.

Time increments can be used for example in high cycle number reactions to allow longer for

enzyme action with successive cycles.

Below is an example of a protocol where the extension step is fixed for the first 15 cycles of a

25-cycle program and increased by 5 seconds/cycle for the next 10 cycles, to compensate for

loss of enzyme activity:

Stage 1: Enter parameters to create:

95oC - 30s

55oC - 30s x 14 Cycles

72oC - 30s

Stage 2: Enter parameters to create:

95oC - 30s

55oC - 30s x 11 Cycles

72oC - 30s + 5s/cycle

Figure 5.3 Programming Time Increments

E D I T I N G A : 0 5 P C R 5 5 C

S T A G E 0 2 S T E P 0 3

T E M P 7 2 : 0

T I M E 0 : 0 0 : 2 0

(1) In the EDIT mode (NEW or EXISTING) move to the temperature step of interest.

↓

↓↓

↓

G R A D 0 0 S T A G E 0 2

R A M P 0 . 0 0 S T E P 0 3

T E M P I N C 0 : 0 0

T I M E I N C 0 : 0 0

(2) Press CONTINUE to access the Advanced Edit screen.

↓

↓↓

↓

G R A D 0 0 S T A G E 0 2

R A M P 0 . 0 0 S T E P 0 3

T E M P I N C 0 : 0 0

T I M E I N C 0 : 0 5

(3) Using the cursor, move through the fields until you reach the desired parameter. Use the

→

→→

→ to toggle between Increase and Decrease in set point time/cycle. Enter the amount by

which the set point time per cycle should change (min:sec) using the number keys. (E.g.

an increase of 5 sec per cycle).

Note: It is possible to alter both the RAMP speed and TEMP increment/decrement

parameters in this screen using the same keys. These altered parameters would also be

executed, simultaneously during your experiment.

↓

↓↓

↓

E D I T I N G A : 0 5 P C R 5 5 C

S T A G E 0 2 S T E P 0 3

T E M P 7 2 : 0

T I M E 0 : 0 0 : 2 0 < A D V >

(4) Using ↓

↓↓

↓ or ENTER to get back to the Editing screen. <ADV> now appears on the

screen indicating an Advanced Edit function has been programmed.

Temperature Advanced Edit Worked Example

Temperature decrements can be used (for example in touchdown cycling reactions) where

the annealing temperature is decreased with successive cycles.

This example shows a protocol where the annealing step is fixed for the first 5 cycles of a 25

cycle program and decreases by 1.0°C/cycle for the next 15 cycles, to reduce specificity and

increase yield as product accumulates (a “touchdown” protocol).

Stage 1: Enter parameters to create:

95oC - 30s

65oC - 30s x 4 Cycles

72oC - 30s

Stage 2: Enter parameters to create:

95oC - 30s

65oC - 30s – 1.0°C/cycle x 16 Cycles

72oC - 30s

Stage 3: Enter parameters to create:

95oC - 30s

50oC - 30s x 5 Cycles

72oC - 30s

Figure 5.4 Programming Temperature Decrements

E D I T I N G A : 0 5 P C R T D

S T A G E 0 2 S T E P 0 3

T E M P 6 5 : 0

T I M E 0 : 0 0 : 3 0

(1) In the EDIT mode (NEW or EXISTING) move to the temperature step of interest.

↓

↓↓

↓

G R A D 0 0 S T A G E 0 2

R A M P 0 . 0 0 S T E P 0 3

T E M P D E C 1.0 0

T I M E I N C 0 : 0 0

(2) Press CONTINUE to access the Advanced Edit screen. Move through the screen until

you reach the TEMP field using the ↓

↓↓

↓ key. Use →

→→

→ to toggle between Increase and

Decrease in set point temp/cycle. Enter the desired value by which the set point temp

per cycle should change (°C) using the number keys (E.g. 1.0°C decrease per cycle).

↓

↓↓

↓

E D I T I N G A : 0 5 P C R T D

S T A G E 0 2 S T E P 0 3

T E M P 6 5 : 0

T I M E 0 : 0 0 : 3 0 < A D V >

(3) Move back to the main step screen using the ↓

↓↓

↓ key. <ADV> will now appear on screen.

Changing Ramp Rates

Ramp rates can be altered in the Advanced Edit screen (refer to Figs.5.4 and 5.5). The default

ramp rate (0.00oC/sec) is “as fast as possible”. The settable range is 0.01oC/sec to 9.99oC/sec,

with the maximum practical setting being 3.00oC/sec with current technologies. The data

entered refers to the ramp rate to the CURRENT step from the PREVIOUS temperature set

point.

For example, cycle sequencing of some targets requires the use of degenerate primers and a

ramp rate set at 1oC/second between the annealing temperature and extension temperature.

5.10 Gradient Feature

This feature is only available to those who have purchased a 0.2ml or 0.5ml gradient block for

temperature gradient cycling. If an attempt to run a gradient program on a non-gradient block

the following screen will appear:

T H I S P R O G R A M

R E Q U I R E S A G R A D I E N T

B L O C K T O B E F I T T E D

< M E N U > T O R E S T A R T

Customers who have purchased a PCR Express prior to 1 December 1998, ensure that:

• Software version 2.0 or later (for use with the PCR Express gradient block) has been

loaded on to your PCR Express chassis.

• Your PCR Express chassis has received a small wiring modification from a Thermo

Hybaid Service Engineer.

If these modifications have not been performed on your PCR Express chassis then your

gradient block will not function. If you are unsure whether these adjustments have been made

to your PCR Express chassis, please contact your local Thermo Hybaid office.

For customers who have purchased a PCR Express after 1 December 1998, all PCR

Express chassis have been modified and are gradient compatible.

The Gradient feature is also accessed through the Advanced Edit function. Simply press the

CONTINUE key from the annealing step in the main programming menu to access the

Advanced Edit screen. After a gradient spread value has been entered in the GRAD section

the number will be displayed on the main programming screen. E.g. <G:10>

The following screen will be displayed when attempting to run a program created under a

previous version of the software, which is incompatible with the new program format in v 2.0

software. The following screen will only appear if an existing program contains time

increments/decrements. This existing program should be edited by returning to the MAIN

MENU and using PROG-EDIT-EXISTING to check that all steps (including other advanced

edit functions) are re-entered as required.

P R O G R A M F O R M A T E R R O R

P L E A S E C O R R E C T

B E F O R E R U N N I N G

< M E N U > T O A B A N D O N

For information on the Gradient Calculator function, refer to section 5.13.

Gradient Programming Worked Example

E D I T I N G A : 0 5 G R A D

S T A G E 0 2 S T E P 0 2

T E M P 4 5 : 0

T I M E 0 : 0 0 : 2 0

(1) In the EDIT mode (NEW or EXISTING) move to the annealing temperature step. The

annealing temperature entered in this step will be the lowest temperature within the

gradient. You must enter a time value as well in order to access the Gradient function in

the Advanced Edit screen. Press CONTINUE to access the Advanced Edit screen.

↓

↓↓

↓

G R A D 1 5 S T A G E 0 2

R A M P 0 . 0 0 S T E P 0 3

T E M P I N C 0 : 0 0

T I M E I N C 0 : 0 0

(2) Enter your required gradient range from 1-15oC.

↓

↓↓

↓

E D I T I N G A : 0 5 G R A D

S T A G E 0 2 S T E P 0 2

T E M P 4 5 : 0 < G : 1 5 >

T I M E 0 : 0 0 : 3 0

(3) The program editing screen will now display the gradient spread depicted as <G:15>. If

a time increment/decrement has been activated then <ADV> will also be displayed on

this screen. Proceed though the programming as discussed in Figure 5.2.

Invalid Gradient Parameters

If the combination of the Set Annealing Temperature and Gradient results in the block

operating outside the temperature limits of 30 to 70oC a ‘TEMP/GRAD INVALID’ message

will briefly be displayed in place of the entered value. E.g. SET TEMP = 70oC and GRAD =

10oC. The SET TEMP will need to be re-entered.

If a temperature is entered that exceeds the 15oC gradient range then a ‘??’ error message will

appear beside the GRAD parameter. A gradient range from 1 – 15oC will need to be re-

entered.

Gradient Calculator Function

Once you have run your samples on an agarose gel, the annealing temperature that

corresponds to your optimum gel result can be determined using the Gradient Calculator

function. Refer to the following figure for an illustration on how to utilise this function.

Figure 5.5 Gradient Calculator Worked Example

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

M A I N M E N U

R U N M A N P R O G O P T S

1. To access the Gradient Calculator move the cursor to OPTS in the MAIN MENU and

press ENTER.

↓

↓↓

↓

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

O P T I O N S M E N U

S E T U P C A L C

2. Move the cursor to CALC and press ENTER.

↓

↓↓

↓

G R A D I E N T C A L C U L A T O R

B L O C K T Y P E 0 . 2 m l

S E T T E M P 4 5 . 0

G R A D I E N T 1 5

3. Specify the block type you have used to optimise your annealing temperatures by using

the ←

←←

← and →

→→

→ keys. Enter the annealing temperature and gradient range used in your

optimisation experiment.

G R A D I E N T C A L C U L A T I O N

C 1 : 4 5 . 4 C 4 : 4 7 . 7

C 2 : 4 5 . 8 C 5 : 4 9 . 4

C 3 : 4 6 . 4 C 6 : 5 1 . 4

G R A D I E N T C A L C U L A T I O N

C 7 : 5 3 . 3 C 1 0 : 5 9 . 0

C 8 : 5 5 . 3 C 1 1 : 5 9 . 7

C 9 : 5 7 . 6 C 1 2 : 6 0 . 2

4. The well temperatures are displayed in sequence, on two screens. Each column

temperature is represented by C1, C2…

E.g.

C1 C2 C3 C4……

5. Press ENTER to access the second screen or use the ↑ and ↓ keys to move back and

forth between the screens. Press ENTER to return to the main menu.

CHAPTER 6

PCR EXPRESS THERMAL CYCLER

Running a Program on the PCR Express

6.1 The RUN Option

The RUN option in the Main Menu enables you to:

• Run a previously stored program.

• Choose the method of temperature control used whilst the program is running.

• Choose whether to run your samples oil free i.e. Heated Lid option.

• Once a program is selected, the program name will be displayed and lid preheating (if

selected) will commence.

If a program is selected and an inappropriate temperature control method is used (e.g.

tube control or simulated tube control for an In Situ interchangeable block module;

simulated slide for an 02/05 module) then a warning message will appear and the

program will be run under the correct mode of control.

6.2 Running a Program on the PCR Express – Short Instructions

Figure 6.1 shows how to run a previously stored protocol. For further information on

temperature control and heated lid functions refer to the sections towards the end of this

chapter. It is possible to edit programs whilst the PCR Express is running a different protocol

(see Section 5.5).

Figure 6.1: Running a Program on the PCR Express

2 0 / 0 7 / 9 9 1 4 : 1 5 : 0 7

I N A C T I V E

M A I N M E N U

R U N M A N P R O G O P T S

1. Press ENTER to select the RUN mode from the MAIN MENU.

↓

↓↓

↓

S E L E C T D I R E C T O R Y :

A : A N I T A D : T H O M A S

B : A L I S O N E : D I A N A

C : D A V E F : H Y B A I D

2. Use the ↑ and ↓ keys to select the source directory.

↓

↓↓

↓

R U N A : 0 1 N O N A M E

H O T L I D A U T O

L O A D I N G A L A R M O F F

E N D R U N A L A R M O F F

3. Enter the program number using the ↑ and ↓ keys, and then press ENTER.

↓

↓↓

↓

R U N A : 0 2 H Y B A I D

H O T L I D O N

L O A D I N G A L A R M O F F

E N D R U N A L A R M O F F

4. Select the heated lid operating method, loading and end run settings, using the → and

pressing ENTER.

↓

↓↓

↓

R U N A : 0 2 H Y B A I D

T U B E

P R E S S > T O C H A N G E

< E N T E R > T O C O N T I N U E

5. Select the control mode using the → and pressing ENTER.

↓

↓↓

↓

P R O G R A M A : 0 2 H Y B A I D

L I D P R E H E A T B E F O R E

A U T O S T A R T

< S T O P > T O A B O R T

6. Cycling commences if the heated lid is selected OFF. If it is ON then the lid will preheat.

If MANUAL start is selected press ENTER to commence cycling.

If AUTO start is selected then it will start automatically.

6.3 Example Run Screens

When a program is running three different run screens can be displayed. These contain

information about the progress of the run together with the temperatures achieved during the

run. This allows the user to monitor the performance of the PCR Express and to determine the

time of the end of the program. These can be accessed by pressing the Ï and Ð arrows, to

scroll through each screen in turn.

These screens can be accessed from the Main Menu by pressing the BLOCK key.

Screen 1

R U N N I N G A : 0 2 H Y B A I D

T E M P 9 5 . 0

B L K 9 6 . 2 T I M E

T U B E 9 5 . 2 0 0 : 0 7

The current block performance screen displays the following:

• Program number and name.

• Current block and tube temperatures.

• Set point (programmed) temperature.

• Time remaining at current setpoint.

Screen 2

R U N N I N G A : 0 2 H Y B A I D

S T A G E 0 1 S T E P 0 2

C Y C L E 1 1 . O F 3 0

M A X 9 7 . 4 M I N 4 4 . 6

The program progress and performance screen displays the following:

• The current stage and step of the running program.

• The total number of cycles completed and remaining.

• The maximum and minimum temperatures achieved during the run in the respective control

mode.

Screen 3

R U N N I N G A : 0 2 H Y B A I D

C O N T R O L T U B E

T I M E N O W 1 0 : 4 3

P R O G R A M E N D 1 2 : 0 3

The estimated run time screen displays the following:

• Temperature control method.

• Time now.

• The calculated run end time (an estimated value which is updated throughout the run).

Screen 4 (During a gradient step)

R U N N I N G A : 0 2 H Y B A I D

T E M P 4 5 . 0 / 5 5 . 0

B L K 4 5 . 2 / 5 5 . 1 T I M E

T U B E 4 5 . 1 0 0 : 0 7

The gradient run screen displays the following:

• TEMP 45.0 = Annealing temperature programmed.

• TEMP 55.0 = Highest annealing temperature programmed.

• BLK = Real time gradient range.

• TUBE 45.1 = Actual sample temperature in position A2 as monitored by the tube

thermistor.

Power Failure Screen

This additional screen appears if the run has been interrupted by a power failure or power

fluctuation severe enough to affect the unit. It contains the following information: -

• The duration of the power failure.

• The stage in the run when the power failure occurred.

End of Run Screen

The PCR Express displays a further screen at the end of the run, this provides the following:

• The program name and number.

• The total run time.

• The maximum and minimum temperatures recorded during the run.

Block Idle Screen

If BLOCK is pressed and there is no run in progress, the block idle screen is displayed.

Error Screens

A number of error screens may be displayed if a fault has been detected in the unit. Contact

the Thermo Hybaid Service Department or your local supplier for advice before attempting to

use the instrument further.

6.4 Temperature Control Options

Crucial to the accurate operation of a thermal cycler is an understanding of the temperature

control methodology.

Active Tube Control (TUBE)

Recommended for all reactions above 20µl volume in 0.5ml and 0.2ml tubes. This type of

control uses the remote thermistor probe mounted in an appropriate tube. A volume of

mineral oil equivalent to the total volume in the reaction tubes (including any oil overlay)

must be present in the control tube (do not use aqueous solutions with the control tube

thermistor).

The thermistor acts as a simple mimic, monitoring the sample temperatures as it changes

during cycling, feeding back this information to the PCR Express processor. This feedback

allows the unit to respond to the sample temperature ensuring that the samples achieve the

exact temperatures and times programmed. To bring the sample to temperature rapidly, the

block is heated/cooled beyond the set temperature for the sample (Figure 6.2). When

designing/transferring to a tube control program it is essential to understand the difference

between tube control and block control on a conventional temperature cycling machine. With

tube control, the actual samples are held at the programmed temperature for the programmed

time. With block control, either on the PCR Express or a thermal cycler without tube control,

there will be a lag between the block reaching target temperature and the sample reaching

target temperature. Thus when transferring protocols from a block control machine the

incubation times may be reduced by up to 50%, and in some cases the temperatures adjusted

slightly.

For Tube Control reactions, check that the tube thermistor is connected and located in the

block (the tube thermistor should be placed in position A2).

When you receive your unit, the thermistor is mounted in a HB-TC-3372 tube for 0.2ml

blocks or a HB-TC-3505 tube for 0.5ml blocks.

NB:Do not disconnect a tube thermistor when a program utilising tube control is in progress.

If this does occur, the program will be abandoned and an error message will be

displayed.

NB:Tube thermistors from TouchDown, OmniGene and Omn-E instruments are not

compatible and CANNOT be used with PCR Express thermal cyclers.

Extension Lead for the Tube Thermistor

The PCR Express is provided with an extension lead for the thermistor. This should only be

used for transferring protocols from instruments that cannot use Active Tube Control. See

Section 7.1 for further details.

Simulated Tube Control (SIM TUBE)

This temperature control method uses an algorithm similar to tube control. However, with

simulated tube control, the block temperature overheat characteristic which is used to

eliminate the sample temperature lag is based on calculated values, rather than the temperature

monitored by the tube thermistor.

Similar considerations apply when transferring protocols from a block control machine as

discussed above, and the extension lead can again be used.

Reactions using Simulated Tube Control do not require the tube thermistor to be connected,

but sample loading and volume details must be entered when prompted by the run screen. For

all tube reactions in a 0.2ml or a 0.5ml thin walled tube, the volume factor is the total

reaction volume in µ

µµ

µl in one well, including any oil overlay. (See Table 6.1) For reactions in

thick walled 0.5ml tubes, use (volume + 50) µl as a good approximation to achieving the same

profile.

Table 6.1: Guidelines for Selecting Temperature Control Method and Entering Volume

Factors

Control Method Loading Factor Volume Factor

Consumable Type 0.5ml Block 0.2ml Block

OmniPlate 96 well

polycarbonate plate

SIM PLATE No. of samples 1-96 vol (µl) x 10 vol (µl)

0.5ml 96 well plate SIM PLATE No. of samples 1-96 vol (µl) -

0.5ml thin walled SIM TUBE No. of tubes 1-48 vol (µl) -

0.5ml thick walled SIM TUBE No. of tubes 1-48 vol (µl) + 50 -

0.3ml thin walled SIM TUBE No. of tubes 1-96 vol (µl) -

0.2ml thin walled SIM TUBE No. of tubes 1-96 - vol (µl)

OmniTube 96 array SIM TUBE No. of tubes (96) - vol (µl)

Simulated Plate Control (SIM PLATE)

This mode of control operates on a similar principle to simulated tube control (see Table 6.1).

However in this case, the control algorithm has been adjusted so that the programmed

temperature is achieved in the volume inside a plate well. The system is optimised for the

0.2ml block and OmniPlate 96.

The use of 96 well plates on the 0.5ml block should be treated with caution. The OmniPlate

96 can and has been used successfully on the 0.5ml block. However, the fit is not optimal,

and as a result there is a significant air gap between the plate and the block itself and the

volume factor should be used to compensate. We recommend initially using a volume factor

equal to 10 x reaction volume, but further optimisation may be necessary.

Figure 6.2 Modes of Control used with the PCR Express

Simulated Slide Control (SIM SLIDE)

a. Active Tube Control

b. Simulated Control (Tube, Plate, Slide)

c. Block Control

This mode of control operates on a similar principle to simulated tube control. However, in

this case, the control algorithm has been adjusted so that the programmed temperature is

achieved on the top surface of a standard microscope slide. The performance of the In Situ

module has been measured using miniature thermistor probes attached to the surface of slides.

Optimum results in terms of overshoot and uniformity across four standard glass microscope

slides (0.8mm-1.0mm thickness) with the humidity chamber in place, have been obtained

using a calibration factor of 200 (the default value). Using a higher calibration accelerates the

approach to target temperature but results in some degree of overshoot. Conversely, a lower

calibration factor slows the approach to target temperature.

Block Control

Controls block temperature as on a conventional dry block machine. We do not recommend

this means of control for thermal cycling due to the variability in thermal profile obtained with

different sample volumes and consumable types.

6.5 Heated Lid Preheat

Once a program and block have been selected, (and calibration factors entered where

appropriate) the program will proceed according to the setup conditions as outlined below.

The heated lid typically takes around 2 minutes to reach operating temperature. During this

time, the block is controlled at 4°C.

WARNING: Both the tops of reaction vessels and the surfaces of the Heated Lid

assembly (in particular the inner surfaces), can become very hot during normal

operation. Touching the surfaces can cause burns. Do not touch the heated plate

without safety gloves.

Heated Lid - Automatic Start

This should be selected for robust cycling reactions, where the reactants can withstand being

incubated for the duration of the preheat (about 2 minutes) without the generation of spurious

products. After the program is selected, the Lid Heating indicator light will switch on,

denoting preheating of the lid. When the lid reaches operating temperature, the

Ready/Working indicator light will change to green and the temperature cycling will start

automatically. In this mode, samples should be loaded and the lid closed before starting the

preheat.

Heated Lid - Manual Start

This should be used for sensitive cycling reactions, where the reactants will not tolerate being

incubated at low temperatures even for a short time, or where all risk of non-specific reactions

must be eliminated. After the program is selected, the Lid Heating indicator light will switch

on, denoting preheating of the lid. When the lid reaches operating temperature, the

Ready/Working indicator light will change to green. An alarm will sound (if activated) and

the ENTER key will need to be pressed to start temperature cycling. In this mode, samples

should be mixed, loaded and the lid closed after the preheat is completed.

If, after 90 minutes, the ENTER key has not been pressed to start a program, the lid will

switch off and the block will return to the idle condition.

No Heated Lid

If the heated lid is switched off (for example to perform experiments with oil overlay present),

the temperature cycling will commence as soon as the program/control/calibration factors

have been entered.

NB: The Lid Heating indicator light will remain off in this mode, and the Ready/Working

light will come on immediately.

6.6. Hold & Pause Function

When entering a program the PCR Express will give you the opportunity to enter a ‘Hold’

temperature at the end of each stage. The samples will be held at this set temperature

indefinitely. The screen will display HOLD during a run. If a “Hold” is inserted between

stages, the program can be advanced to the next stage by pressing CONTINUE. If a “Hold”

is inserted at the last stage, pressing CONTINUE will switch to the run summary screen.

Common uses of the Hold step include the following: -

• Inserting an initial 95oC incubation at the start of the protocol to perform the ‘Hot Start’

procedure. After the enzyme has been added, pressing CONTINUE will advance the

program into the cycling part of the protocol.

• A final low temperature (4-10oC) hold for the end of overnight runs. Although unnecessary

for the vast majority of protocols, some scientists prefer to have this step included.

• A final 72oC incubation to ensure completion of the final extension step of a reaction.

Pressing PAUSE during a cycling program will pause the program at the current or next target

temperature within the step. Pressing CONTINUE will continue the countdown for the step.

6.7 Aborting Programs

The program will run to completion unless interrupted by the pressing of either the PAUSE or

STOP keys whilst the appropriate run screen is displayed.

Pressing the STOP key once will display a verification screen (the program continues while

this is displayed). Pressing STOP again aborts the program. Pressing MENU displays the

Main Menu and continues the program.

6.8 Program Completion

At the end of the program the END OF RUN screen will be displayed. In this case, the heated

lid will be switched off automatically.

The alarm (if selected) will sound and the block will remain at 20°C for 30 minutes to drive

the heated lid plate temperature to ambient.

If a final HOLD temperature has been specified, the heated lid (if selected) will remain on.

For most thermal cycling applications a final HOLD at elevated temperature is not

necessary. Extended high temperature hold steps can lead to evaporation and

condensation problems, particularly with polycarbonate plates.

CHAPTER 7

PCR EXPRESS THERMAL CYCLER

Troubleshooting

Check the volume in the tube thermistor

Check the volume of mineral oil in the control tube (a vial of suitable mineral oil is provided

(alternatively Sigma molecular biology-grade mineral oil, M5904 or equivalent can be used).

Do not use aqueous solutions in the control tube. Too much oil in the control tube will

result in overshoots in the sample tube temperatures, whilst too little oil there will result in a

time lag in the samples achieving temperature. The volume of oil in the control tube should

match that in the reaction tubes, (including any oil overlay). Repeated overshoots at the

denaturation temperature during temperature cycling, will reduce the activity of the

thermostable enzyme resulting in poor yields of product. The correct position for the control

tube is position A2.

Check location of thermistor within the control tube

Always ensure the thermistor probe is located centrally in the control tube and immersed in

the liquid. If pushed against the side it will be measuring the temperature of the

microcentrifuge tube and not the sample temperature.

Check the fit of the tube in the block

The PCR Express block accommodates most types of reaction tubes. The tube thermistor

supplied with the PCR Express is mounted on an OmniTube, which should be changed

periodically, as the fit of the tube will deteriorate with time. Reaction tubes should be

distributed evenly in the block. If you are using a reaction tube that has not been

recommended, check its fit in the PCR Express block before use. You should also remount

the thermistor probe in this tube to ensure that your samples and the control tube are matched.

Check through the program

Before running a program, use the VIEW function to check that the correct combination of

temperature and program number have been entered.

Runs using Simulated Control Methods

1. Simulated Tube

Enter the number of samples, including the thermistor and the total reaction volume per tube

including any oil overlay. 50µl should be added to the volume factor if thick walled tubes are

used.

Use a setting of 96 samples and the correct reaction volume including oil overlay if a

polypropylene OmniTube 96 is used.

2. Simulated Plate

0.2ml blocks

For 96 well microplates, (including OmniPlate 96), on a 0.2ml block, the volume factor

entered is the individual sample volume. (NB: Polypropylene OmniTube 96 should be run

under Sim Tube Control).

0.5ml blocks

For OmniPlates on a 0.5ml block, the volume factor entered is the total sample volume

multiplied by 10 (to a maximum of 500). This accommodates the non-optimal fit of the

OmniPlate 96 in the 0.5ml block. Other 96 well plates, for example the Costar ThermowellH,

may be used with lower multiples of volume, but these need to be individually determined.

384 well blocks

For 384 well blocks the individual well volume should be used for the volume factor

3. Simulated Slide

For 0.8mm - 1mm thick glass slides using simulated slide control, the calibration factor is 200

(default value), other thicknesses will need optimization.

Check maximum and minimum values achieved during the run. This will give an indication

of unusual temperature performance.

Power failure during a run

A message will appear on the main menu screen. The machine will either restart automatically

when power is restored, or the program will be abandoned, as specified by the user on the SET

UP menu screen. Viewing the run screens for the block will indicate the time of the power

failure, and where applicable the time the run resumed.

7.1 Transfer of protocols from a block control machine to tube control using

the thermistor lead extension

The different modes of control should be considered before transferring protocols directly.

E.g., consider a temperature cycling protocol consisting of 1 minute at 95°C followed by 1

minute at 65°C, repeated 30 times. Using block control, the actual sample temperature is at

95°C for just 30 seconds at each step, a total of 15 minutes overall. In contrast tube control

will result in precise one minute incubations at each step, a total of 30 minutes at the target

denaturation temperature. Even though tube control gives a more accurate representation of

the program, transferring such a protocol directly could result in lower yields because the

enzyme is exposed to the high temperature for significantly longer, thus reducing its activity in

later cycles.

The most accurate way to transfer protocols is to use the control tube of the PCR Express as a

temperature probe in the block control machine as follows:

1. Set the PCR Express to run a single program at a set temperature for an extended time.

(e.g. 37°C for 4 hrs), ensuring that the heated lid is switched off and the instrument is

set to block control. This enables the tube thermistor to be used remotely.

2. Connect the thermistor lead extension to the thermistor control tube and plug it into

the PCR Express.

3. Place the thermistor tube probe into the corresponding thermistor probe socket of the

PCR Express, and locate the tube in a well of the block control machine running the

required protocol.

4. After a short equilibration interval, the display on the PCR Express will indicate the

sample tube temperature, which should be noted at regular time intervals (e.g. 10

seconds, for a number of cycles.) The actual length of time spent at each of the

denaturation, annealing and elongation stages should be recorded, as well as any

temperature overshoot values where the maximum/minimum temperature exceeds the

target temperature or undershoots where the target temperature is not actually reached.

5. The temperature profile that the samples in the block control machine actually achieve,

rather than simply the block temperature, can be used to program your PCR Express.

Optimisation of protocols

The capability of the PCR Express programming enables protocol optimizations to be

performed very rapidly. Typically, temperature cycling protocols may consist of three distinct

stages:

1. Denaturation at an elevated temperature (usually 90-95°C).

2. Annealing at a temperature dictated by the melting temperature (Tm) of the

oligonucleotides.

3. Enzymatic activity at a temperature dictated by the optimum temperature of the

thermostable enzyme being used.

These three steps are typically repeated for twenty to thirty cycles depending on the amount of

starting template.

Denaturation

The denaturation step at each cycle must be sufficient to denature the target DNA completely,

including G-C rich regions. However, the effect on the enzyme activity of repeated high

temperature incubations should also be considered. An extended initial denaturation step, (3

minutes, 95°C, before enzyme addition) will denature complex high molecular weight DNA

template, but for later cycles this should be reduced to a maximum of 30 seconds at 92-95°C.

Optimisation of the denaturation step is the most critical factor when transferring a protocol

from a block control machine to tube control.

Annealing

The annealing temperature depends on the size and nucleotide composition of the

oligonucleotides used. In general it varies between 50°C and 70°C and as a rough guide

should be 5°C below the Tm. This may be calculated approximately using the following

formula:

Tm = 2 x (A + T) + 4 x (G + C)

A difference in the annealing temperature of as little as 1°C can affect the specificity of a

reaction, it is therefore recommended that a range of temperatures is tested to optimise the

annealing temperature for each primer and template combination.

Extension

The extension temperature is largely dependent upon the optimum temperature of the enzyme

chosen and is usually in the range 70-75°C (see data sheet from manufacturer). The time

required depends on the length of product being synthesised.

CHAPTER 8

PCR EXPRESS THERMAL CYCLER

Maintenance

8.1 General Cleaning

1. All surfaces of the PCR Express system and Heated Lid should be cleaned regularly

with a soft cloth, hot water and a mild detergent.

2. It is important to thoroughly dry all surfaces after cleaning.

3. The PCR Express is not intended for use with aggressive chemicals and on no account

should organic solvents be used to clean this equipment.

4. Dampened cotton buds can be used to remove dirt and debris from individual wells.

The wells should be kept clean to maintain optimum heat transfer performance.

8.2 Decontamination

When 35S labelled nucleotides are thermally cycled they break down into lower molecular

weight forms which are highly volatile and can leach through the walls of tubes and microtitre

plates thus contaminating the block and possibly the heater plate of the heated lid.

We therefore do not recommend the use of 35S labels, as replacing a dangerously

contaminated block is expensive.

If 35S labels are used, we recommend the following to minimize contamination.

1. Use a mineral oil overlay in all reactions, even when the Heated Lid is used.

2. If using tubes, use only the thick walled variety.

3. Use the thermal cycler in a fume hood, to minimize air contamination.

4. If using microtitre plates, coat the under surface with a thin layer of mineral oil.

5. If radioactivity must be used, the thermal cycling block and Heated Lid surfaces can be

decontaminated using a 10 % v/v solution of Neutracon (Decon Lab Ltd, Conway Street

Hove, East Sussex BN3 3LY Tel: +44(0) 1273-739241, Fax: +44(0) 1273-722088) or

PCC-54 (Pierce Eurochemie B.V Holland). Complete decontamination is unlikely, but

low level counts can be achieved by repeated application of a fresh solution of 10% v/v

Neutracon to the "Hot" area.

All Control Chassis, Block Module, and Heated Lid components coming into contact with

radioactivity should be decontaminated before re-use or transportation. In the event of

returning a contaminated item please contact Thermo Hybaid’s Service Department so that the

appropriate handling arrangements can be made.

Thermo Hybaid recommends that if radioisotopes are to be used, equipment

must be located in a designated Radiation Area. Local Radiation Safety

procedures must be followed at all times.

The use of 35S labelled nucleotides is not covered under our warranty agreement

and requires special service arrangements.

8.3 Protection to the User

The PCR Express has been designed with operation safety in mind. In the rare event of an

instrument failure, three levels of protection are built in to ensure the unit “fails safe”. First,

the software sets normal operating ranges for the block and lid. Should this fail; electrical

circuitry is in place to ensure that safe temperatures are not exceeded. In the unlikely event of

this failing, thermal fuses are fitted to shut off the power supply to damaged components.

The unit is fitted with an internal lithium battery containing a hazardous substance. This

should be replaced with the original type and disposed of with care.

8.4 Protection of the Instrument

Fuses

The PCR Express mains power inlet is fitted with two T6.3A fuses (20mm x 5mm). If

necessary these may be replaced by a qualified person.

8.5 Tube Thermistor Care

The tube thermistor assembly ensures that the programmed temperature profile is accurately

and reproducibly achieved within all sample tubes. As a ‘sample mimic’, it is important that

the thermistor is as close a representation as possible to the biological samples. To maintain

accuracy and longevity of the tube thermistor Thermo Hybaid recommends the following:

1) Do change the tube thermistor annually. It may be necessary to change the thermistor

more often under heavy use (e.g. frequent removal of the thermistor from the tube).

2) Do check that the mineral oil volume is the same as the reaction volume including any

oil overlay.

3) Do check and replace the control tube if it is showing signs of thermal degradation.

4) Do use the same type of tube for the thermistor tube as for the biological samples.

5) Do make sure the sensor part of the thermistor probe is centrally located at the base of

the tube and is fully covered by mineral oil.

6) Don’t use aqueous solutions in the thermistor tube.

7) Don’t remove the control tube from the cap assembly by pulling the wire; gently lever

the tube from the cap.

8) Don’t kink the thermistor wire or crush the sensor part of the thermistor probe end.

9) Don’t remove the thermistor assembly from the instrument by pulling on the wire, pull

from the plug.

CHAPTER 9

PCR EXPRESS THERMAL CYCLER

Technical Specifications & Ordering Information

Description PCR Express with 0.5ml Block PCR Express with 0.2ml Block

Catalogue Number HB-PX-05-220/110 HB-PX-02-220/110

Block Capacity 48 x 0.5ml tubes

96 x 0.3ml tubes

1 x 96 well plate

96 x 0.2ml tubes

1 OmniPlate 96

Temperature Control

Available

Tube control

Simulated tube control

Simulated plate control

Block control

Tube control

Simulated tube control

Simulated plate control

Block control

Performance

Block Temperature

Range

4°C - 99°C 4°C - 99°C

Block Heating Rate Up to 3°C/Sec Up to 3°C/Sec

Block Cooling Rate Up to 2°C/Sec Up to 2°C/Sec

Precision Control 1°C 1°C

Block Uniformity + 0.4°C within 15 secs + 0.4°C within 15 secs

Heated Lid

Temperature Range

95°C - 120°C 95°C - 120°C

Display Resolution 0.1°C 0.1°C

Standard Accessories Tube Thermistor 0.5ml

(HB-PX-TTM05)

Tube Thermistor 0.2ml

(HB-PX-TTM02)

Interchangeable

Block Modules

HB-PX-B05 HB-PX-B02

PCR Express Chassis HB-PX-220/110

Description PCR Express with In Situ

Block

PCR Express with 384

Well Block

Catalogue Number HB-PX-FB-220/110 HB-PX-384-220/110

Block Capacity 4 x microscope slides

(76 x 26 x 1mm)

1 x OmniPlate 384

Temperature Control

Available

Simulated slide control

Block control

Simulated plate control

Block control

Performance

Block Temperature Range 4°C - 99°C 4°C - 99°C

Block Heating Rate Up to 3°C/Sec Up to 3°C/Sec

Block Cooling Rate Up to 2°C/Sec Up to 2°C/Sec

Precision Control 1°C 1°C

Block Uniformity + 0.4°C within 15 secs + 0.4°C within 15 secs

Heated Lid Temperature

Range

95°C - 120°C* 95°C - 120°C

Display Resolution 0.1°C 0.1°C

Standard Accessories Humidity Chamber

Interchangeable Block

Modules

HB-PX-BFB HB-PX-B384

PCR Express Gradient Cyclers

Description PCR Express with 0.5ml

Gradient Block

PCR Express with 0.2ml

Gradient Block

Catalogue Number HB-PX-G05-220/110 HB-PX-G02-220/110

Block Capacity 48 x 0.5ml tubes

96 x 0.3ml tubes

1 x 96 well plate

96 x 0.2ml tubes

1 OmniPlate 96

Temperature Control

Available

Tube control

Simulated tube control

Simulated plate control

Block control

Tube control

Simulated tube control

Simulated plate control

Block control

Performance

Block Temperature Range 4°C - 99°C 4°C - 99°C

Block Heating Rate Up to 3°C/Sec Up to 3°C/Sec

Block Cooling Rate Up to 2°C/Sec Up to 2°C/Sec

Precision Control 1°C 1°C

Block Uniformity + 0.4°C within 15 secs + 0.4°C within 15 secs

Heated Lid Temperature

Range

95°C - 120°C 95°C - 120°C

Display Resolution 0.1°C 0.1°C

Standard Accessories Tube Thermistor 0.5ml

(HB-PX-TTM05)

Tube Thermistor 0.2ml

(HB-PX-TTM02)

Interchangeable Block

Modules

HB-PX-BG05 HB-PX-BG02

PCR Express Chassis HB-PX-220/110

PROGRAMMING (all unit variants)

Number of programs 99

Number of directories 6

Maximum number of program stages 10

Maximum number of steps per stage 10

Maximum programmed dwell time 9hr 59 mins 59 secs

Time increment/decrement Yes

Temp increment/decrement Yes

Temperature ramping Yes

Pause facility Yes

Autostart facility Yes

Run “end time” calculations Yes

File protection Yes

Output RS232

Alphanumeric programming Yes

Gradient Software Yes

Power 550W

Dimensions (WxDxH) 240mm x 390mm x 250mm

Weight 8.9kg

Working Conditions

Ambient temperatures of 4°C to 35°C

Power requirements: 550W at 115/230V a.c. + 10% and 50/60Hz.

Satisfies the requirements of BS EN 61010-1:1993.

NB: When the PCR Express temperature cycler is removed from a cold room, it should be

left to equilibrate for 2-3 hours to avoid condensation.

9.1 Consumables

Consumables Pack

Size

Description Catalogue Number

Sealing Systems

TD Tape 50 Sealing tape for polycarbonate plates HB-TD-TAPE50

TDX Tape 100 Sealing tape for polypropylene plates HB-TD-TAPE100

Compression Pad 1 Foam pressure pad for use with tape sealing

system

HB-TD-SFOAM

OmniSeal TD Mat 5 Reusable 96 well sealing mat HB-TD-MTSRS5

Plastic Ware

Consumables Pack

Size

Description Catalogue

Number

Plates

OmniPlate 96 25 Polycarbonate 96 well plate HB-TR3-MT

OmniPlate 96 Lid 25 Polycarbonate lids HB-TR3-MTL

OmniFast 96 25 Polypropylene 96 well plate HB-TC-8002N

OmniFast 384 50 Polypropylene 384 well plate HB-TC-3840N

OmniTube 96 25 Single piece polypropylene plate HB-TC-6002N

Tubes

OmniTube 0.2ml 1000 0.2ml individual tubes with integral domed caps HB-TC-3372N

OmniTube 0.2ml 1000 0.2ml individual tubes with integral flat caps HB-TC-6202N

OmniTube 0.5ml 1000 0.5ml individual tubes with integral domed caps HB-TC-4895N

OmniTube 0.5ml 1000 0.5ml individual tubes with integral flat caps HB-TC-3505N

OmniStrip 0.2ml 2000 0.2ml strips of 8 tubes & caps HB-TC-2662N

OmniStrip 0.3ml 2000 0.3ml strips of 8 tubes & caps HB-TC-4043N

Racked OmniTubes 25 For 0.3ml 96 well plates (caps not included) HB-TC-4073N

OmniTube Caps 2400 For all 0.2ml and 0.3ml OmniTube products HB-TC-6022N

We recommend that domed cap tubes are used when the temperature control is set to

Active Tube and flat cap tubes are used under Simulated Tube Control.

Polycarbonate can be affected by contact with formamide, DMSO and other organic

solvents; these should therefore be avoided when using the polycarbonate OmniPlate 96.

APPENDIX I

PCR EXPRESS THERMAL CYCLER

Software Upgrade via RS232

Thermo Hybaid issues software upgrades on a regular basis as new programming features

become available. So that you can benefit from future innovations, the PCR Express software

can be upgraded via an RS232 connection to the serial point of the PC using the cable

provided.

Software is distributed free via Thermo Hybaid’s Internet site (http://www.hybaid.com), or

can be obtained on disk (PC) from your local Thermo Hybaid representative.

To upgrade the software you will need:

• A PC with a free COM1 port (9 way connector).

• Communications cable (supplied with your PCR Express).

• The PCR Express to be upgraded.

Upgrade Instructions (Dos)

• Ensure that the PCR Express is switched off.

• Connect the PC to the PCR Express using the cable supplied. One end should be

connected to the COM1 port of the PC; the other should be connected to the 9-way

connector on the underside of the PCR Express (next to the fan).

• Whilst simultaneously depressing the PAUSE and CONTINUE keys, switch on the PCR

Express which will respond with three short bleeps and display a “READY TO LOAD

SOFTWARE" message. The PAUSE and CONTINUE keys may then be released.

• On the PC, at the DOS prompt, type:

• A:UPLOADSA A:PCRE0200.BIN

• The PC will display the status of the upload as it progresses.

• When the upload is complete, the PC will display the message. Your PCR Express is now

ready to use. Switch off the PCR Express and then switch back on in the normal manner

(do not depress the PAUSE and CONTINUE keys).

Upgrade Instructions (Windows 3.1)

• Insert Setup Disk 1 in drive A or Drive B.

• In Program Manager, click on File on the menu bar, click on Run…

• Type in the command line: a:\setup.exe if you inserted Setup Disk 1 in drive A, or type

b:\setup.exe if you inserted Setup Disk 1 in drive B. Click the OK button.

• Follow the on-screen instructions given by the installation program.

• To upgrade your PCR-Express, double click the Pcrexp icon in the Windows Program

Manager. Follow the on-screen instructions.

Upgrade Instructions (Windows 95)

• Insert Setup Disk 1 in drive A or Drive B.

• Click on Start and then Run…

• Type in the command line: a:\setup.exe if you inserted Setup Disk 1 in drive A, or type

b:\setup.exe if you inserted Setup Disk 1 in drive B. Click the OK button.

• Follow the on-screen instructions given by the installation program.

• To upgrade your PCR-Express, click Start, select Programs, point to the Pcrexp folder

and then click Pcrexp. Follow the on-screen instructions.

Upgrade Instructions (Internet)

Instructions will be given on Thermo Hybaid’s Internet site.

It is important that the self test is not bypassed when first powering up a machine

containing new software.

Verify that the self test completes correctly and that the correct software version is displayed

on the SETUP MENU screen. The software upgrade process is now complete.

APPENDIX II

PCR EXPRESS THERMAL CYCLER

Sealing Systems: The OmniSeal TD Mat & TD Tape

Overview

Thermo Hybaid offers two sealing systems to suit individual preferences. The TD Tape is a

single use adhesive tape suitable for use with 96 well and 384 well systems, whereas the

OmniSeal TD Mat is a re-usable silicone rubber mat designed for 96 well systems only.

How to use the TD/TDX Tape

TD Tape and TDX Tape are unique single use sealing systems for oil free thermal cycling in

96 well and 384 well plates which prevents cross contamination between wells. After a

thermal cycling reaction TD or TDX tape can be removed from the plate with ease.

TD Tape

Green in colour and designed for use with polycarbonate plates such as OmniPlate 96.

TDX Tape

Clear in colour and designed for use with polypropylene plates such as OmniTube 96,

OmniFast 96 or OmniFast 384.

TD and TDX tape cannot be interchanged, as the TDX tape will bind irreversibly to

polycarbonate.

To secure contact with the heated lid of the thermal cycler the TD and TDX tapes must be

used in combination with the reusable TD Compression Pad.

Sealing a 96/384 Well Plate

1. The tape can be applied to 96/384 well plates by positioning over one of the short edges

and peeling back the lining material, allowing the adhesive layer to fall on to the plate.

This should be possible without introducing creases. However, before heating, the

adhesive is soft enough to be repositioned without adverse effects.

2. The tape should be firmly anchored by pressing over each well. This can be done using a

soft roller or by finger pressure.

3. Once in the machine, the Compression Pad (HB-TD-SFOAM) must be placed on top of

the sealed plate. The Compression Pad performs a dual function. It ensures that the tops

of the sealed well reach the correct temperature and under compression it ensures the

sealing between wells is intact.

Adding the TD Tape

Place a sealed 96 well/384 well plate on the machine. Select the “Plates” setting and close the

lid.

Removing The TD Tape

Prior to removing the TD Tape/TDX Tape from a plate, ensure there is no condensation of the

solution inside the wells or on the plugs of the tape by either:

1. Removing the 96 well plate from the block and cooling to 4°C.

2. Cooling down the PCR block to 4°C (if possible).

3. Heating the sample to 35°C for 30 minutes.

This will minimise the risk of well-to-well contamination when removing the TD Tape from

the 96 well plate.

The TD Tape is most easily removed while the 96 well plate is in a rack or still on the

machine. The sheet should be peeled back from one corner diagonally across the plate using

a single smooth action. The TD Tape is easily removed and therefore is especially suitable

for applications which require additions of reagents part way through the reaction, for

example when performing reverse transcription and amplification in two stages.

Resealing Using TD Tape

TD Tape is designed for single use. Once heated and compressed, the backing conforms to

the plate and cannot be easily repositioned. Re-use is therefore not advised.

OmniSeal TD Mat

Cleaning & Sterilisation Procedures

The OmniSeal TD Mat (Catalogue N°: HB-TD-MT-SRS-5) is used to seal 96 well plates

when using the PCR Express Heated Lid. Mats can be cleaned and sterilised using the

procedures described below.

Soak for 1 minute in either 10% hypochlorite solution, or 0.1M hydrochloric acid solution and

then rinse with distilled water. Dry inside an oven at up to 80°C if required. Autoclave at

121°C for 15 minutes.

Sealing a 96 Well Plate

OmniSeal TD Mats have 96 plugs in the underside. They are spaced so that they fit into the

wells of a 96 well plate.

The plugs are shaped to expand sideways in order to seal all 96 wells of a 96 well plate, when

sufficient pressure is exerted to the upper surface of the mat by the PCR Express Heated Lid.

Figure 10.1: Showing how the OmniSeal TD Mat seals the wells of a 96 well plate.

Removing the OmniSeal TD Mat

To minimise the risk of well-to-well contamination, remove the OmniSeal TD Mat from the

96 well plate whilst the plate is in a rack or on the machine.

Re-usability of the OmniSeal TD Mats

The OmniSeal TD Mat can be re-used at least 5 times. Repeated washing and autoclaving of

the Mats causes them to crack around the edges. When this starts to happen, they should be

discarded.

NB: The number of times an OmniSeal TD Mat can be re-used is reduced considerably if it

is cleaned with alcohols or detergents, or if exposed to UV irradiation.

Limitation of Microtitre Plate Operations

Some users have reported loss of volume when using microtitre plates for thermal cycling.

Recent experiments performed at Thermo Hybaid have demonstrated that volume loss is

independent of sample volume and occurs through the sides of the polycarbonate microtitre

plate (all manufacturer plates tested) and is not due to poor sealing. Typically volume loss of

3µl per well in a 30-cycle reaction can be expected.

If you are working with small sample volumes it may be advisable to switch to polypropylene

consumables instead.

APPENDIX III

PCR EXPRESS THERMAL CYCLER

In Situ Block Application Notes

Overview

The PCR Express In Situ module with flat block has been designed for the precise control of

temperature on up to four standard microscope slides (dimensions 76mm x 26mm x 1mm).

Flat blocks are supplied with a Humidity Chamber, which can be used to reduce sample

drying.

Temperature Control

The In Situ block can perform all the control functions of the standard PCR Express reaction

tube block with the exceptions of Active Tube Control and Simulated Tube Control. Instead,

the Simulated Slide Control option is used which minimises the time lag between the block

reaching target temperature and the sample on the surface of the slide achieving target

temperature. At the start of running a program on an In Situ module the SIM SLIDE option

should be selected as the control mode (see Figure 5.1). The Heated Lid is not operational

under this control mode.

The performance of the In Situ module has been measured using miniature thermistor probes

attached to the surface of slides. Optimum results across four standard slides (1mm thickness)

with the humidity chamber in place have been obtained using a calibration factor of 200.

Using a higher calibration factor accelerates the approach to target temperature, but results in a

degree of overshoot. Conversely, a lower calibration factor slows the approach to target

temperature, but minimises any overshoot. A calibration factor of zero would be equivalent to

block control when using SIM SLIDE.

Protocol Transfer

When transferring protocols from a conventional 'block control' machine, it is important to

consider the effect of using PCR Express's 'Simulated Slide' control. On conventional thermal

cyclers, the programmed temperatures commonly refer to the temperature achieved by the

block and not the microscope slide. Consequently, a sample on the top surface of a glass slide

will be significantly cooler than the block temperature. The PCR Express’s 'Simulated Slide'

control overcomes this problem by using an algorithm to ensure the temperature achieved by

samples on the surface of the slides is as close as possible to the programmed temperature.

In practice this difference in achieved temperature between different control systems is most

pronounced at the denaturation step. As a guide, we recommend that when transferring

protocols from a conventional thermal cycler to the PCR Express In Situ, the denaturation

temperature is reduced by 3°C.

Programming

Programming and operation of the In Situ module are identical to the standard PCR Express

tube modules (see Chapter 5) with the exceptions previously noted and also no heated lid

operation is supported. For simple fixed temperature incubations of the slides, manual control

can be used (Chapter 4). For more complex multi-step incubations or for temperature cycling

reactions use Programmed Operation (Chapter 6).

Humidity Chamber

The polycarbonate Humidity Chamber has been designed to reduce drying out of the sample

on the slides. For accurate temperature performance, the In Situ module should be used with

the Humidity Chamber in place and the lid closed.

• Fill the reservoirs with water.

• Pre-heat the block with the Humidity Chamber in place. This allows the reservoir to warm

up so that evaporation of the solution can begin. Alternatively, preheat the reservoir

solution to the incubation temperature required.

• For thermal cycling with extended/high temperature incubations, it is important to seal the

reagents under the cover slip. Thermo Hybaid recommends the use of EasiSeal sealing

frames. These are available in three sizes (25µl - HB-OS-SSEZ1E, 65µl - HB-OS-

SSEZ2E, and 125µl - HB-OS-SSEZ3E). They will completely seal the specimen area to

prevent drying.

NB: If a petroleum based rubber compound is used for sealing cover slips in place, the

compound should be allowed to dry out completely before use with this system. If complete

drying is not allowed, the solvent vapour will damage the surface of the Humidity Chamber.

More information on the use of In Situ applications using Thermo Hybaid equipment can be

obtained from the Thermo Hybaid In Situ Hybridization Guide, which is available free upon

request.

APPENDIX IV

PCR EXPRESS THERMAL CYCLER

Comparative Performance Data between Thermo Hybaid Ambient & Sub-

Ambient Block Systems

Although there are fundamental differences between the methods of heating and cooling for

these different block systems, in the majority of cases, direct transfer of protocols will be

possible. This is because the temperature and time control system is similar for the PCR

Express, TouchDown, Omn-E and OmniGene systems, even though the performance and

accuracy characteristics are different. There are some cases however, when the biological

performance of the two instruments for a given cycling protocol will be different. One

obvious example is for reactions with annealing temperatures close to ambient. Less obvious

is the effect of default ramp rates on other stages of the reaction (see Table 7.1).

Table 7.1: Block Ramping Characteristics of Ambient and Sub-ambient Units

CYCLING STAGE AMBIENT SUB-AMBIENT NOTES

Extension-Denaturation Essentially linear to

within 5°C of

setpoint. (Max. up

to 2°C/second)

Essentially linear to

within 5°C of

setpoint. (Max. up to

3°C/second)

Ambient denaturation

setpoint times may be

able to be decreased (e.g.

5 sec/cycle) compared to

sub-ambient because of

the latter’s faster

approach to setpoint

Denaturation-Annealing Faster the further

away from ambient.

(Max. up to

2°C/second (90-

80°C)- Effect of

decrease minimal in

operating range to

ambient+10°C)

Essentially linear to

within 5°C of

setpoint for settings

down to 20°C.

(Max. up to

1.8°C/second)

Fundamentally, the sub-

ambient unit will give

better temperature

control for newer

applications requiring

annealing temperatures

close to ambient

Annealing-Extension Essentially linear to

within 5°C of

setpoint. (Max. up to

2°C/second)

Essentially linear to

within 5°C of

setpoint. (Max. up to

3°C/second)

The more rapid heating

rate of the sub-ambient

units from the annealing

temperature may need to

be slowed using ramp

rate control to mimic the

temperature profile of a

reaction optimised on an

ambient version

APPENDIX V

PCR EXPRESS THERMAL CYCLER

Glossary of Terms

Advanced Edit Allows the adjustment of the following:

1) Incrementation/decrementation of time and/or

temperature on a cycle-by-cycle basis.

2) Control of temperature ramping between set

points.

Block Control The temperature of the cycling block is monitored

and controlled by the thermistor mounted on the

block. Because of the time lag between the block

and sample reaching temperature we recommend

that tube control is used.

Block Module The interchangeable assembly comprising sample

block, Peltier array, heatsink and control thermistor.

Control Chassis The main body of the machine, incorporating

keypad, control and power functions, fan and

display. The Heated Lid is fitted to the control

chassis.

Copy Copy is used to make identical copies of stored

programs, prior to editing.

Edit Edit is used to create new programs or to change

existing programs.

Erase Erase is used to delete programs or create extra space

for new protocols.

GRADIENT CALCULATOR

Software

Software for use in calculating optimized annealing

temperatures after gradient cycling.

HOLD A HOLD step may be specified at the end of a stage.

Samples are held at this temperature until

CONTINUE is pressed to resume the program. This

function can be used to hold samples at a fixed

temperature while a reagent is added before

temperature cycling starts.

In Situ Module The PCR Express Flat Block, for performing In Situ

reactions on up to four microscope slides.

Loading Factor To compensate for differing numbers of samples,

enter the number of tubes for each cycling run.

MAN

Manual Operation

Manual operation is used for single temperature

incubations under block control. The incubation will

proceed at the set temperature until the STOP button

is pressed; or until a new temperature is specified.

Menu The menu key allows the user to return to the main

menu at any time without making changes in the

programming/operation of the unit.

OPTS Allows the accessing of SETUP options or

GRADIENT CALCULATOR Software

New Temperature A new temperature may be specified during a

manual incubation step. The manual program is

interrupted and the sample temperature rapidly

changes to the newly specified temperature.

Peltier Device A thermoelectric device incorporating a bismuth

telluride semi-conductor crystal array. On passing a

current through the crystal, one surface of the crystal

is heated, the other cooled. Reversing the current

reverses the heat flow.

Power Failure The PCR Express has the facility to restart after a

mains power supply failure. There are two set up

options for restarting after a power failure:

1. Resume program at step that power failure

occurred.

2. Abandon program at power failure step.

One of the above should be specified using the

SETUP menu.

PROGRAM Select PROG from the main menu to access the

programming menu.

Ramp Rate

(Temperature Ramping)

Ramping precisely controls the rate of change of

sample temperature (ºC/sec). This is useful for

limiting the rate of change of temperature, to allow

partial extension of short or degenerate primers.

RUN The RUN Option allows the user to run a stored

program on the block

Sample Volume When using simulated tube control methods, the

sample is entered to ensure precise block heating and

cooling.

SET UP This function allows the default settings of the PCR

Express (set day and time, power restart option and

screen brightness) to be modified.

Simulated Plate Control Simulated Plate Control incorporates an algorithm to

reduce time to reach target temperature, using

precise overshoots in block temperature for each

setpoint. Refer to Section 5.2 for instructions on

how to use this control option.

Simulated Slide Control Simulated Slide Control incorporates an algorithm to

reduce the time to target temperature when

performing temperature cycling reactions using

microscope slides on an In Situ block.

Simulated Tube Control Simulated Tube Control incorporates an algorithm to

reduce the time to reach target temperature, using

precise overshoots in block temperature for each

setpoint. The calculated sample temperature inside

sample tubes and block temperature are displayed

during the run.

Stage One stage of a program consists of one or more steps

up to a maximum of 10. A stage may be repeated for

temperature cycling. Up to ten stages may be used in

one program, and stage-to-stage linking is automatic.

Step A step consists of a programmed temperature and

time interval. Time increment and ramp rate may

also be specified if required. Enter zero for each

heading to specify the last step of a particular stage,

and enter zero for each heading at the first step of the

final stage.

Sub-ambient Block The aluminium block used on sub-ambient PCR

Express systems. This uses Peltier devices for

heating and cooling. Operating range: 4°C to 99°C.

TEMP INC/DEC

Temperature

Increment/Decrement

May be used to increase/decrease a temperature set

point at successive cycles. E.g. a decrement of 0.1°C

will give 60, 59.9, 59.8, 59.7.... °C.

This is useful for touchdown PCR reactions where

stringency at the annealing step is decreased as the

reaction proceeds.

Thermistor A thermistor is a resistor whose resistance changes

with temperature. It can therefore be used as a very

accurate temperature probe with small liquid

volumes.

TIME INC/DEC

Time Increment/Decrement

May be used to change a time interval to each repeat

cycle of a specific step. E.g. an increment of 10

seconds on a 60 second step will give time intervals

of 60, 70, 80, 90, 100....seconds. This is useful when

increasing an incubation step to allow for the

depletion of an enzyme.

Touchdown PCR A gene amplification procedure where the annealing

temperature is high (e.g. 65°C) to achieve high

specificity at the start of the reaction. It can then be

reduced with successive cycles (by e.g. 0.5°C/Cycle)

to increase yield once high stringency is no longer

required.

TUBE

(Active) Tube Control

This type of software control is dependent upon the

external thermistor probe located in the microfuge

tube. This allows very accurate monitoring and

control of sample tube temperature. This feedback

control loop allows the transition to target

temperature to be accelerated by creating a

temperature gradient between the block temperature

and the tube temperature.

HEATED LID A standard fitting which allows oil free cycling in

0.2, 0.3, 0.5ml tubes and 96/384 well plates. The

auto-height adjusting heated plate in contact with the

top of the reaction vessels maintains the temperature

above 100ºC, preventing evaporation of the sample.

View The View function allows the contents of programs

to be accessed.

APPENDIX VI

PCR EXPRESS THERMAL CYCLER

Pre-Set Programs on the PCR Express

Programs coded into the F:HYBAID Directory of the PCR Express memory can be used

directly or as building blocks for other protocols using the COPY function.

PROGRAM F:90 3T_PCR

Stage 1 Step 1 94°C0:01:00 x 1

Stage 2 Step 1 94°C0:00:30

Step 2 55°C0:00:30

Step 3 72°C0:00:30 x 30

Stage 3 Step 1 72°C0:05:00 x 1

Hold 4°C

PROGRAM F:91 2T_PCR

Stage 1 Step 1 94°C0:01:00 x 1

Stage 2 Step 1 94°C0:00:10

Step 2 68°C0:00:10 x 30

Stage 3 Step 1 72°C0:05:00 x 1

Hold 4°C

PROGRAM F:92 LONGPCR

Stage 1 Step 1 94°C0:02:00 x 1

Stage 2 Step 1 94°C0:00:10

Step 2 65°C0:00:30

Step 3 68°C0:10:00 x 10

Stage 3 Step 1 94°C0:00:10

Step 2 65°C0:00:30

Step 3 68°C0:10:00 + Time Inc. 0:20/cycle x 20

Stage 4 Step 1 68°C0:07:00 x 1

PROGRAM F:93 CYCSEQ

Stage 1 Step 1 94°C 0:01:00 x 1

Stage 2 Step 1 94°C 0:00:10

Step 2 50°C 0:00:10

Step 3 60°C 0:04:00 x 25

Hold 10°C

PROGRAM F:94 TD_PCR

Stage 1 Step 1 94°C 0:01:00 x 1

Stage 2 Step 1 94°C 0:00:30

Step 2 65°C 0:00:30

Step 3 72°C 0:00:30 x 4

Stage 3 Step 1 94°C 0:00:30

Step 2 65°C 0:00:30 + Temp DEC-1.0°C /cycle

Step 3 72°C 0:00:30 x 16

Stage 4 Step 1 94°C 0:00:30

Step 2 50°C 0:00:30

Step 3 72°C 0:00:30 x 5

Stage 5 Step 1 72°C 0:05:00 x 1

PROGRAM F:95 RTPCR37

Stage 1 Step 1 37°C 1:00:00

Step 2 95°C 0:10:00 x 1

Hold 4°C

Stage 2 Step 1 95°C 0:00:30

Step 2 55°C 0:00:30

Step 3 72°C 0:00:30 x 40

Stage 3 Step 1 72°C 0:05:00 x 1

PROGRAM F:96 RTPCR65

Stage 1 Step 1 65°C 1:00:00

Step 2 94°C 0:01:00

Stage 2 Step 1 94°C 0:00:15

Step 2 65°C 0:00:30 x 40

Stage 3 Step 1 65°C 0:07:00 x 1

PROGRAM F:97 RAMP

Stage 1 Step 1 94°C 0:01:00 x 1

Stage 2 Step 1 94°C 0:00:30 Ramp 1.0°C/Sec

Step2 55°C 0:00:30 Ramp 1.0°C/Sec

Step 3 72°C 0:00:30 Ramp 1.0°C/Sec

Stage 3 Step 1 72°C 0:05:00 x 1

PROGRAM F:98 DIGEST

Stage 1 Step 1 37°C 4:00:00 x 1

PROGRAM F:99 CUT/KIL

Stage 1 Step 1 37°C 4:00:00

Step 2 95°C 0:15:00 x 1

Hold 4°C

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