Caitlin Smith has a B.A. in biology from Reed College, a Ph.D. in neuroscience from Yale University, and completed postdoctoral work at the Vollum Institute.
Thermal cyclers, also known as thermocyclers or PCR machines, are important basic instruments relied upon in nearly all molecular biology labs and frequently used in cell biology and other labs, too. Thermocyclers change the temperature of samples at precise times and intervals in order to amplify tiny amounts of genetic material by PCR. Furthermore, these changes have to be fast and exacting for high-quality results. In addition to being a central genetics research tool, thermocyclers and PCR are used in applications such as cloning DNA for sequencing genes, diagnosing diseases and identifying people genetically. Choosing a thermal cycler is best done with five key criteria in mind, so that you can find the instrument that best fits your lab.
1. Sample throughput.
With so many thermocycler models available today, consider the type of throughput your lab will need. For small numbers of samples, so-called personal PCR machines that sit unobtrusively on your benchtop or desk may be perfect. Their small sizes do not mean lesser quality—some of these small models have faster run times than their larger counterparts, because their diminutive size facilitates faster changes in temperature. One can even find small models that are portable for field use. On the other hand, labs that need to conduct high-throughput PCR may benefit not only from individual thermocyclers that can hold as many samples as possible but also from thermocycler models that can be networked together and controlled from one instrument.
2. Heating-block format.
The heating block in which the PCR sample tubes incubate is available in different formats. The first considerations are how many samples the block holds and the sample volumes. The most basic thermocyclers may offer only one choice. Therefore, if you suspect you will need flexibility in sample numbers and size in the future, check out the many other options available. Some vendors offer models that have blocks in different sizes/capacities.
Other vendors offer thermocyclers with flexible block formats consisting of multiple, interchangeable units. Some models even offer different temperature controls for different units. This can be helpful for conducting multiple experiments simultaneously or for optimizing PCR conditions.
3. Thermal gradient
Programmable thermal gradients are useful for finding optimal PCR conditions (for example, in primer annealing). Simple optimization usually requires only the basic gradient function of a simple, single gradient across the heating block (i.e. each row ramps to a different temperature). Also available, though, are models that allow you to program zones of different temperatures into the gradient block, which allows for multiple experiments or conditions in a single run time.
4. Maximum ramp rate.
A thermocycler’s maximum ramp rate is the maximum rate at which its heating block can change temperature. A faster ramp rate is a good thing. Usually the faster ramp rates are on the order of 5°C or 6°C per second (faster models usually have heating blocks made of silver, which conducts heat better than other materials typically used for thermocycler blocks). Another important consequence of the ramp rate is the length of your entire protocol, because ramp rate determines how long it will take your thermocycler to complete a specified number of cycles.
5. High-tech lids.
Specialized thermocycler lids can head off two problems that may otherwise wreak havoc with your PCR reactions—especially if you are using smaller sample volumes. These problems will have a greater effect on the concentration of reaction components when using small sample volumes, leading to erroneous results. One problem is evaporation, which can be ameliorated by lids with special sealing mechanisms. Another problem is condensation on the inside of the PCR tube top. Tubes at the edges and corners of the block may be especially vulnerable to this source of potential variation.
Looking forward
Lastly, an important general point to consider is your lab’s future needs. For example, some thermocycler models offer the possibility to upgrade to a real-time thermal cycler for quantitative PCR. Also take into account changes you might envision in throughput, sample size or types of PCR, and you will be making a wise choice for your current experiments as well as those you will be running down the road.
The image at the top of the page is Bio-Rad's DNA Engine Dyad Peltier Thermal Cycler.