= Polymerase chain reaction
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= PCR amplification
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{synonym}
The <polymerase chain reaction> amplifies a selected <DNA> region using repeated copying steps. Amplified material can be examined by <DNA sequencing>; appropriate template controls help distinguish a new rearrangement from material already present in the starting preparation.
The essential trick is to choose two <PCR primers> on opposite <DNA> strands with their extendible $3'$ ends facing into the same interval. A <DNA polymerase> extends each <PCR primer> $5'\to3'$; the resulting <DNA> can itself become a template. The <amplicon> is therefore selected by two opposed <PCR primers>, rather than by the <DNA polymerase> recognizing a named <gene>. This makes <PCR amplification> useful for inspecting one interval within a much larger <genome>. Here PCR means <polymerase chain reaction>; the statistical abbreviation <PCR> means <principal component regression>.<Polymerase Chain Reaction (PCR) by Addgene>[Background Information: two primers, template-directed copying and product verification]{ref}
For a deliberately tiny <nucleotide sequence> example, display the upper strand as $5'\text{-}\mathrm{ACGT}\text{-}\mathrm{GGAATT}\text{-}\mathrm{CAGC}\text{-}3'$. The left <PCR primer> is $5'\text{-}\mathrm{ACGT}\text{-}3'$ and binds the lower strand. The right <PCR primer>, written in its own $5'$-to-$3'$ direction, is $5'\text{-}\mathrm{GCTG}\text{-}3'$: the <reverse complement> of CAGC. It binds the upper strand and extends leftward in the drawing. With flanks outside this interval, the bounded <amplicon> contains $4+6+4=14$ <base pairs>, including both <PCR primer> sequences. These four-<nucleotide> <PCR primers> illustrate direction and counting only; they are not a proposed experimental design.
\Image[/pcr-opposed-primers-strand-cycles.png]
{title=Opposed <PCR primers> define the <amplicon> through successive copying cycles}
{description=Original schematic, not molecular imaging. The upper panel follows separation, binding and $5'$-to-$3'$ extension on the two original <DNA> strands. The lower panel follows one selected lineage: cycle 1 makes a strand with one primer-defined end; cycle 2 copies it to make the first strand bounded at both ends; cycle 3 copies that bounded strand to make a bounded duplex. Other products are omitted. Primer colors identify the two <PCR primers>, not different <nucleobases>; extensions continue beyond the second site when the available template extends farther.}
A useful way to understand the <polymerase chain reaction> is to separate recognition from construction. <Base pairing> positions a <PCR primer>; a <DNA polymerase> then joins new <nucleotides> onto that existing strand. The <PCR primer> becomes part of the copied <DNA>, rather than merely marking a place for an independent strand to start. A <PCR thermal cycle> repeatedly exposes templates, positions starting ends and permits construction. This makes <DNA> copying possible outside <biological cells>, with the chosen <PCR primers> specifying which interval is repeatedly accessible.
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