from Wittwer CT and Farrar JS (2011) in PCR Troubleshooting and Optimization

Before thermostable polymerases were used in PCR, thermal cyclers were unwieldy instruments with integrated fluidics to add fresh enzyme after each denaturation. Taq polymerase greatly reduced the engineering complexity of thermal cyclers, requiring only temperature cycling but not liquid handling. It did not take long before a variety of thermal cycling solutions appeared. Instruments progressed rapidly from laboratory oddities to mainstream commodities. Some early homemade examples changed the temperature of stationary reactions with flowing water or robotically transferred samples between constant temperature water baths (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). However, water has some drawbacks. Due to its large thermal mass a great amount of energy and time is required to heat or cool water to a specific temperature. In contrast, air has a very low thermal mass and was used in some early systems (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). Many thermal cyclers now use Peltier elements and metal blocks for heating and cooling.

Today, PCR hardware and reagents are commonplace in research and diagnostic laboratories. The instruments have evolved to fill a variety of batch size and time-to-result needs. Thermal cycling concerns now focus on issues of speed, temperature uniformity, sample volume and increased throughput. Many thermal cycling solutions, heat-stable polymerases, and commercial PCR master mixes that include all components except primers and template DNA are available commercially.

A big step in PCR automation was connecting the amplification and detection stages to control PCR product contamination. Laboratories can be plagued by false positive results if products from a prior reaction find their way into a future reaction with the same primers. This contamination is usually controlled by separating pre- and post-amplification processes and careful attention to reaction preparation (Wittwer and Farrar, 2011 in PCR Troubleshooting and Optimization). Another solution is to automate both amplification and detection in a closed-vessel system, eliminating PCR product exposure to the environment. The best solution is to amplify and analyze at the same time by real-time PCR and/or melting analysis.