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Newsletter

Features of Real-time PCR Platforms and qPCR Machines

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications
In weighing up the pros and cons of the different real-time PCR machines available for your laboratory, factors to consider include: supported chemistries; multiplex capability for that chemistry; throughput; flexibility; format; easy-of-use and robust software package; reproducibility; speed; size; technical support; customer support and not least the cost, not only of the initial equipment outlay and servicing but also the associated cost of consumables and reagents. It is also possible to 'try before you buy', most companies will provide a loan machine. It is wise to test a few of these once you have narrowed down your choice. User experiences should not be overlooked and there are a number of useful websites and forums where you can address you questions and queries.
Real-Time PCR
Edited by: Nick A. Saunders and Martin A. Lee
Provides both the novice and experienced user with an invaluable reference to a wide-range of real-time PCR technologies and applications and supplies detailed technical insights into the underlying principles, methods and practice of real-time PCR.
"an invaluable reference" (Doodys); "wide range of real time PCR technologies" (Food Sci Technol Abs) read more ...
Real-Time PCR in Food Science
Edited by: David Rodríguez-Lázaro
An indispensable manual on real-time PCR for scientists in the food industry and for anyone involved in the detection of foodborne pathogens.
"I would recommend this text to anyone" (AJMS); "an excellent, detailed guide" (Emerg. Inf. Dis.) read more ...

The following PCR machines are compared for various features to help you decide which instrument is most suitable for your needs. Please scroll down the page to see the various platforms.

  • Applied Biosystems: ABI 7300, ABI 7500, ABI 7500 Fast, ABI 7900 Fast HT with automation accessory, ABI StepOne
  • Roche: LightCycler 480, LightCycler 1.5, LightCycler 2.0
  • Stratagene: Mx4000, Mx3000P, Mx3005P
  • Cepheid: SmartCycler
  • Corbett: Rotor-Gene 6000
  • Eppendorf: Mastercycler ep realplex
  • BioRad: MiniOpticon, MyiQ, Opticon2, Chromo4, iQ5

Company

Applied Biosystems

Applied Biosystems

Model

ABI 7300

ABI 7500

Laser/Lamp

tungsten halogen lamp

tungsten halogen lamp

Detector

CCD camera

CCD camera

Thermocycling

peltier element block

peltier element block

Excitation spectrum

single excitation filter

five excitation filters

Filters/detection channels

4-position filter wheel: FAM/SYBR Green I, VIC/JOE, NED/TAMRA and ROX

5-position filter wheel: FAM/SYBR Green I, VIC/JOE, NED/TAMRA/Cy3, ROX/Texas Red and Cy5 dyes

Format

96-well plates or 0.2 ml tubes

96-well plates or 0.2 ml tubes

Time (40 cycles)

1.75 hours

1.75 hours

Reaction Volume

20-100 μl

20-100 μl

Fluorescence Chemistry

hydrolysis probes and SYBR Green I, other chemistries possible but not supported

hydrolysis probes and SYBR Green I, other chemistries possible but not supported

Multiplexing Supported

4-plex

5-plex

Passive Reference

ROX (optional)

ROX (optional)

Dimensions (H x W x D)

34 x 49 x 45 cm

34 x 49 x 45 cm

Weight

29 Kg

34 Kg

Other features

primer/probe design software included

primer/probe design software included

PCR mastermix kits, parameter specific kits

PCR mastermix kits and parameter specific kits

Assay by Design and Assay on Demand Services

Assay by Design and Assay on Demand Services

Software: gene expression analysis, absolute quantification, allelic discrimination and plus/minus assays

Software: absolute quantification, relative quantification, allelic discrimination, isothermal and plus/minus assays

SDS v1.4 21CFRp11 Module assists with 21CFRp11 compliance

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Applied Biosystems

Applied Biosystems

Model

ABI 7500 Fast

ABI 7900 Fast HT with automation accessory

Laser/Lamp

tungsten halogen lamp

argon ion laser

Detector

CCD camera

CCD camera

Thermocycling

peltier element block

peltier element 9700 block

Excitation spectrum

five excitation filters

488 nm

Filters/detection channels

5-position filter wheel: FAM/SYBR Green I, VIC/JOE, NED/TAMRA/Cy3, ROX/Texas Red and Cy5 dyes

500-660 nm continuous wavelength detection,

SYBR Green I, FAM, VIC, JOE, NED, ROX,  TAMRA, TET

Format

fast 96-well plates optimised for 10 μl reactions

96- and 384-well plates (interchangeable blocks)

Time (40 cycles)

< 30 mins

33 mins (96-well plate) or 52 mins (384-well plate)

Reaction Volume

10-30 μl

5-20 μl

Fluorescence Chemistry

hydrolysis probes and SYBR Green I, other chemistries possible but not supported

hydrolysis probes and SYBR Green I, other chemistries possible but not supported

Multiplexing Supported

5-plex

6-plex

Passive Reference

ROX (optional)

ROX (optional)

Dimensions (H x W x D)

34 x 49 x 45 cm

64 x 125 x 84 cm

Weight

34 Kg

114 Kg

Other features

primer/probe design software included

primer/probe design software included

PCR mastermix kits, parameter specific kits

PCR mastermix kits, parameter specific kits

Assay by Design and Assay on Demand Services

Assay by Design and Assay on Demand Services

Software: absolute quantification, relative quantification, allelic discrimination, isothermal, melt curve analysis and plus/minus assays

Software: absolute quantitation, relative quantitation, allelic discrimination, isothermal, plus/minus assays, high throughput SNP genotyping and gene expression

SDS v1.4 21CFRp11 Module assists with 21CFRp11 compliance

SDS v1.4 21CFRp11 Module assists with 21CFRp11 compliance

Robotic plate un/loading for up to 84 plates, high throughput: real-time PCR >5000 wells per day and end-point 30,000 wells every 3 hours

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Applied Biosystems

Roche

Model

ABI StepOne

LightCycler 480

Laser/Lamp

LED

high intensity xenon lamp

Detector

3 emission filters and photodiode

CCD camera

Thermocycling

peltier element block

peltier element block incorporating Therma-Base technology

Excitation spectrum

480 nm

430-630 nm, 5-position filter wheel: 450, 483, 523, 558 and 615 nm

Filters/detection channels

3 filters: SYBR Green I/FAM, VIC/JOE and ROX

6 position filter wheel: 500, 533, 568, 610, 640, 670 nm

Format

48-well plates, 0.1 ml individual or 8-strip tubes

96- and 384-well plates (interchangeable blocks)

Time (40 cycles)

< 40 mins

< 1 hour (96-well plate) or < 40 mins (384-well) plate

Reaction Volume

10-30 μl

10-100 μl (96-well plate), 3-20μl (384-well plate)

Fluorescence Chemistry

hydrolysis probes, SYBR Green I, other chemistries possible but not supported

hydrolysis probes, hybridisation probes, simple probes, SYBR Green I, UPL

Multiplexing Supported

3-plex

3-plex hybridisation and 6-plex hydrolysis probes

Passive Reference

ROX (optional)

Not required

Dimensions (H x W x D)

24.6 x 51.2 x 42.7 cm

54.5 x 60 x 60 cm

Weight

23.6 Kg

55 Kg

Other features

primer/probe design software included

primer/probe design software available

Touchscreen, wizard driven software with networking capabilities

System compatible with 21 CFR part 11 requirements

PCR mastermix kits

PCR mastermix kits, parameter specific kits

Software: standard curve, relative standard curve, comparative Ct (DDCt), allelic discrimination, melt curve analysis and plus/minus assays

Software: absolute quantification, Tm calling, colour compensation, qualitative detection, statistical analysis, relative quantitation, high-resolution melting, genotyping, LIMS/bar-code module

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Roche

Roche

Model

LightCycler 1.5

LightCycler 2.0

Laser/Lamp

LED

LED

Detector

3 photodetection diodes

6 photodetection diodes

Thermocycling

heated air

heated air

Excitation spectrum

470 +/- 10 nm

470 +/- 10 nm

Filters/detection channels

3 channels: 530, 640, 710 nm

6 channels: 530, 560, 610, 640, 670, 710 nm

Format

32 glass capillaries

32 glass capillaries

Time (40 cycles)

30 mins

30 mins

Reaction Volume

20 μl

20 μl or 100 μl

Fluorescence Chemistry

hybridisation probes, hydrolysis probes, molecular beacons, SYBR Green I

hybridisation probes, hydrolysis probes, molecular beacons, SYBR Green I, simple probes, UPL

Multiplexing Supported

2-plex hybridisation probes

4-plex hybridisation and 2-plex hydrolysis probes

Passive Reference

Not required

Not required

Dimensions (H x W x D)

45 x 30 x 40 cm

45 x 30 x 40 cm

Weight

20 Kg

20 Kg

Other features

primer/probe design software available

primer/probe design software included

PCR mastermix kits, parameter specific kits

PCR mastermix kits, parameter specific kits

Software: absolute quantitation, genotyping analysis, melting curve analysis, multiplex analysis

Software: absolute quantification, relative quantification, genotyping analysis, Tm calling analysis, multiplex analysis, plus/minus assays

Relative quantification software available

Nucleic acid quantitation

Conforms to European directive for in vitro diagnostic medical devices 98/79/EC.

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Stratagene

Stratagene

Model

Mx4000

Mx3000P

Laser/Lamp

Quartz tungsten halogen lamp

Quartz tungsten halogen lamp

Detector

4 PMTs

1 scanning PMT

Thermocycling

Solid-state resistive/convective peltier hybrid block

Solid-state peltier-based block

Excitation spectrum

4 interchangeable filter wheels in the range 350-750 nm

4 user defined matched filter wheels in the range 350-750 nm

Filters/detection channels

4 interchangeable filter wheels in the range 350-830 nm

4 user defined matched filter wheels in range 350-700 nm (default: FAM, Hex, ROX, Cy 3)

Format

96-well plates, 0.2 ml tubes, 8 x 0.2ml strips

96-well plates, 0.2 ml tubes, 8 x 0.2ml strips

Time (40 cycles)

< 1.5 hours

< 1.5 hours

Reaction Volume

10-50 μl

10-50 μl

Fluorescence Chemistry

hydrolysis probes, fret probes, molecular beacons, Scorpions, Amplifluor, SYBR Green I

hydrolysis probes, fret probes, molecular beacons, Scorpions, Amplifluor, SYBR Green I

Multiplexing Supported

4-plex

4-plex

Passive Reference

Optional ROX

Optional ROX

Dimensions (H x W x D)

76 x 46 x 51cm

33 x 46 x 43 cm

Weight

50 Kg

20 Kg

Other features

PCR mastermix kits

PCR mastermix kits

System compatible with 21 CFR part 11 requirements

System compatible with 21 CFR part 11 requirements

Software: gene expression analysis, allelic discrimination, melting curve analysis

Software: gene expression analysis, allelic discrimination, melting curve analysis

Integrated computer

Integrated computer

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Stratagene

Cepheid

Model

Mx3005P

SmartCycler

Laser/Lamp

Quartz tungsten halogen lamp

4 high intensity LEDs

Detector

1 scanning PMT

Silicon photodetectors

Thermocycling

Solid-state peltier-based block

Resistive heating of ceramic plates with forced-air cooling

Excitation spectrum

5 user defined independent filter wheels in the range 350-750 nm

4 channels (450-495, 500-550, 565-590, 630-650)

Filters/detection channels

5 user defined independent filter wheels in the range 350-700 nm (default: FAM, Hex, ROX, Cy5, Cy 3)

4 channels (510-527, 565-590, 606-650, 670-750)

(default: FAM, Cy3, TET, Alexa 532, Texas Red, Cy5, Alexa 647 and Eva Green)

Format

96-well plates, 0.2 ml tubes, 8 x 0;2ml strips

16 proprietary tubes

Time (40 cycles)

< 1.5 hours

20 - 40 mins

Reaction Volume

10-50 μl

25 or 100 μl

Fluorescence Chemistry

hydrolysis probes, fret probes, molecular beacons, Scorpions, Amplifluor, SYBR Green I

hydrolysis probes, molecular beacons, Eclipse probes, Amplifluor and Scorpion primers, SYBR Green I

Multiplexing Supported

5-plex

4-plex

Passive Reference

Optional ROX

Not required

Dimensions (H x W x D)

33 x 46 x 43 cm

30 x 30 x 25 cm

Weight

20 Kg

10 Kg

Other features

PCR mastermix kits

PCR mastermix kits and parameter specific kits

System compatible with 21 CFR part 11 requirements

Random access (16 independently programmable reactions site)

Software: gene expression analysis, allelic discrimination, melting curve analysis

Software: gene expression analysis, allelic discrimination, melting curve analysis and endpoint

Integrated computer

Compact and portable for field use

Modular system - flexibility to expand in multiples of 16 module units up to 96 reaction sites

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

Corbett

Eppendorf

Model

Rotor-Gene 6000

Mastercycler ep realplex4

Laser/Lamp

6 high power LEDs

96 LEDs

Detector

PMT

2-channel PMT

Thermocycling

Resistive heater with air cooling and centrifugation

Gradient peltier element block

Excitation spectrum

365, 470, 530, 585, 625, 680 nm,

470 nm

Filters/detection channels

460, 510, 555, 610, 660, 712 nm

520 / 550 / 580 / 605 nm

Format

36 0.2 ml or 72, 0.1 ml plastic tubes; 72 or 100 well Gene-Disc plastic rings

96-well plates, 0.2 ml tubes

Time (40 cycles)

40 mins

30 mins

Reaction Volume

10-100μl, 10-50μl, 15-50μl, 10-25μl

5-100μl

Fluorescence Chemistry

hydrolysis probes, molecular beacons, hybridisation probes, SYBR Green I

Open system all formats supported, except hybridisation probes

Multiplexing Supported

6-plex

4-plex

Passive Reference

Not required

Not required

Dimensions (H x W x D)

27.5 x 37 x 42

39.6 x 26 x 41 cm

Weight

14 Kg

24 Kg

Other features

Centrifugal rotary design

PCR mastermix kits

Software: HRM (high-resolution melt), end-point, association / disassociation (i.e. melting / annealing) kinetics, relative expression and nucleic acid concentration measurement

Software: raw data, melting curve analysis, quantification/relative quantification, allele discrimination, endpoint, +/- assays.

Gradient range of 24°C

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

BioRad

BioRad

Model

MiniOpticon

MyiQ

Laser/Lamp

48 LEDs

Tungsten-halogen lamp

Detector

2 photodiodes

12-bit CCD camera

Thermocycling

MJ Mini peltier element block

iCycler peltier element block

Excitation spectrum

470-500 nm

475-495 nm

Filters/detection channels

523-543 nm

540-700 nm

515-545 nm

Format

48 well PCR plate, 6 x 8 tube strips

96 well plates, 0.2ml tubes

Time (40 cycles)

< 40 mins

< 40 minutes

Reaction Volume

10-100 μl (20 μl recommended)

10 - 100 μl

Fluorescence Chemistry

hydrolysis probes, molecular beacons, SYBR Green I

hydrolysis probes, molecular beacons, SYBR Green I

Multiplexing Supported

2-plex

Single-plex

Passive Reference

Not required

Fluorescein

Dimensions (H x W x D)

33 x 18 x 32

39 x 29 x 58

Weight

6.8 Kg

17.6 Kg

Other features

PCR mastermix kits

PCR mastermix kits

Software: allelic discrimination, gene expression analysis, melting curve analysis

Software: allelic discrimination, gene expression analysis, melting curve analysis, end point detection, absolute quantification

Connect 4 instruments to 1 PC

Optional software for 21 CFR part 11 compliance

Gradient range of 16°C

Gradient range of 25°C

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

BioRad

BioRad

Model

Opticon2

Chromo4

Laser/Lamp

96 LEDs

4 LEDs in photonics shuttle

Detector

Dual PMTs

4 photodiodes

Thermocycling

DNA Engine peltier element block

DNA Engine Dyad Disciple peltier element block

Excitation spectrum

470-505 nm

450-650 nm

Filters/detection channels

523-543, 540-700 nm

515-730 nm

Format

96-well plate, 8 x 0.2ml strip tubes

96-well PCR plate or 96 x 0.2 ml tubes

Time (40 cycles)

< 40 mins

< 40 mins

Reaction Volume

10-100 μl (20 μl recommended)

10-100 μl (20 μl recommended)

Fluorescence Chemistry

hydrolysis probes, molecular beacons, SYBR Green I

hydrolysis probes, molecular beacons, SYBR Green I

Multiplexing Supported

2-plex

4-plex

Passive Reference

Not required

Not required

Dimensions (H x W x D)

60 x 34 x 47 cm

37 x 24 x 35

Weight

29 Kg

12.6 Kg

Other features

PCR mastermix kits

PCR mastermix kits

Software: allelic discrimination, gene expression analysis, melting curve analysis

Software: allelic discrimination, gene expression analysis, melting curve analysis

Gradient range of 24°C

Customisable filter sets

Modular design for maximal flexibility, 2 x 96 Dyad

Gradient range of 24°C

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications

Company

BioRad

Model

iQ5

Laser/Lamp

Tungsten halogen lamp

Detector

12-bit CCD camera

Thermocycling

iCycler peltier element block

Excitation spectrum

5 filter positions in range 475-645 nm

Filters/detection channels

5 filter positions available in range 515-700 nm, 2 provided

Format

96- or 384-well plate, 8 x 0.2ml strip tubes

Time (40 cycles)

< 40 minutes

Reaction Volume

15-100 μl

Fluorescence Chemistry

hydrolysis probes, molecular beacons, hybridisation probes, SYBR Green I

Multiplexing Supported

5-plex

Passive Reference

Fluorescein

Dimensions (H x W x D)

36 x 33 x 62 cm

Weight

17.6 Kg

Other features

PCR mastermix kits

Software: allelic discrimination, gene expression analysis, melting curve analysis, end point detection, absolute quantification

Gradient range of 25°C

Optional software for 21 CFR part 11 compliance

Abbreviations: LED, light emitting diode; CCD, charge-coupled device camera; PMT, photomultiplier tube; UPL, universal probe library

from Julie Logan, Kirstin Edwards and Nick Saunders in Real-Time PCR: Current Technology and Applications