PCR Instrumentation

The first consideration for choosing the right thermal cycler is often the goal of the PCR reaction and what experiment will be performed downstream.

• If you often run new PCR assays and need to troubleshoot different annealing temperatures frequently, choose a thermal cycler with a thermal gradient that can be used to optimize the yield and specificity of an assay in a single run.
• If you are running high-throughput genotyping experiments you may prefer to use a high-performance cyclers with fast ramping speeds to shorten run times
• If you perform PCR to clone DNA fragments you may prefer to use a thermal cycler that can run large reaction volumes or that is compatible with 0.5 ml tubes

The second consideration is the number of users and the sample throughput.

• 48-well cyclers are often used as personal systems
• 96-well cyclers are standard for many laboratories
• Dual 48/48 well cyclers allow 2 independent protocols to be run simultaneously when there are many people using an instrument
• Multi-bay cyclers are popular for high-throughput laboratories, although multiple single-bay cyclers are also a good option; some are networkable or have USB ports to transfer protocols between thermal cyclers

A third consideration is flexibility when considering current and future experiments.

• Thermal cyclers with interchangeable blocks allow various formats such as 96-well, 384-well, dual 48/48-well to be swapped easily without the purchase of an entire new system
• Some instruments also allow upgradeability to real-time PCR
• Networkable thermal cyclers allow satellite units to be daisy-chained to a control unit to expand throughput when needed

Lastly, it is wise not to forget the importance of software features and overall ease of use, since these factors can greatly impact the time spent training new users, and getting started with a run regardless of the application or throughput of the laboratory.

Thermal Cycler Selection Chart

Feature	C1000 Touch™	S1000™	T100™
Peltier-effect technology	•	•	•
Upgrade to real-time PCR	•
Interchangeable sample blocks	•	•
Number of wells	96, 96 deep, dual 48, or 384	96, 96 deep, dual 48, or 384	96
Gradient capability	•	•	•
Graphical user interface	•		•
Fast PCR protocol templates	•	•	•
Choice of temperature control mode	•	•	•
Power failure restore	•	•	•
Programmable ramp rates	•	•	•
Networking capability	•	•
Reports on cycler use and performance	•	•	•
Adjustable heated lid	•	•
Full-skirted plate compatibility	•	•