Polymerase chain reaction (PCR) is a technique used to exponentially amplify a specific target DNA sequence, allowing for the isolation, sequencing, or cloning of a single sequence among many. PCR was developed in 1983 by Kary Mullis, who received a Nobel Prize in chemistry in 1993 for his invention. The polymerase chain reaction has been elaborated in many ways since its introduction and is now commonly used for a wide variety of applications including genotyping, cloning, mutation detection, sequencing, microarrays, forensics, and paternity testing.
Typically, a PCR is a three-step reaction. The sample containing a dilute concentration of template DNA is mixed with a heat-stable DNA polymerase, such as Taq polymerase, primers, deoxynucleoside triphosphates (dNTPs), and magnesium. In the first step of PCR, the sample is heated to 95–98°C, which denatures the double-stranded DNA, splitting it into two single strands. In the second step, the temperature is decreased to approximately 55–65°C, allowing the primers to bind, or anneal, to specific sequences of DNA at each end of the target sequence, also known as the template. In the third step, the temperature is typically increased to 72°C, allowing the DNA polymerase to extend the primers by the addition of dNTPs to create a new strand of DNA, thus doubling the quantity of DNA in the reaction. This sequence of denaturation, annealing, and extension is repeated for many cycles, resulting in the exponential amplification of the template DNA. As the DNA polymerase loses activity or the dNTPs and primers are consumed, the reaction rate reaches a plateau.
This section includes considerations for the proper design and optimization, analysis, and troubleshooting of polymerase chain reactions, as well as descriptions of the required PCR instrumentation and reagents.