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The PCR is an in vitro technique that allows one to clone a stretch of DNA in the test tube, without the necessity of cloning and subcloning in bacteria. In doing so, it has also facilitated a host of applications (eg. VNTR) and variations (eg. RAPD).

To perform a typical PCR reaction, some sequence information about two regions of your DNA of interest is required so that appropriate primers may be synthesized. The two primers, each typically about 15-20 nucleotides in length, are usually designed so they are 200-2000 bp apart, one hybridizing to one strand of dsDNA, the other hybridizing to the other strand such that both primers are oriented with their 3' ends pointing towards each other.

The first step of the cycle is denaturation, a so-called hot-start, brought about by briefly heating to 93 degrees, which dissociates the target DNA into its two strands prior to addition of DNA polymerase. The dissociated target strands, the primers, dNTPs and DNA polymerase are then incubated together first at a temperature that allows the primers to hybridize to the target strands (usually somewhere between 40 and 55 degrees), and then at a temperature which facilitates elongation by a thermostable DNA polymerase such as Taq polymerase (usually ~72 degrees); this allows a first round of synthesis to occur on each of the DNA templates.

At the start of the second temperature cycle the products are dissociated by a 93 degree denaturation step, separating the newly formed strands from the template DNA, and the material is passed through the second and third steps of the cycle. This time primers hybridize not only to the original strands but also to the newly synthesized strands where they bring about elongation, but only as far as the other primer (because that is where their structure originated).

In the third and subsequent cycles, amplification by the majority of molecules occurs between the regions bounded by the two primers leading, over 30 or so cycles, to an increase in the number of cloned molecules by geometrical progression (although there will still be amplification by arithmetic progression with respect to the original target material and to the first strands synthesized). The result, after 30 cycles of amplification, is the production of {2³⁰ - (2 x 30)} (ie. over one hundred million copies) of the DNA sequence in between, and including, the two primers.