= Primer
{disambiguate=molecular biology}
A \b[primer] is an existing nucleic-acid strand that supplies an extendable end for template-directed synthesis. In <DNA replication>, a <DNA polymerase> extends a suitably paired $3'$ end rather than starting an arbitrary new strand from two free <nucleotides>. The <primer-template junction> therefore identifies both an initiation site and an orientation. The primary characterization of <bacteriophage T4 DNA polymerase> explicitly requires a template and primer for synthesis.<T4 DNA Polymerase by New England Biolabs>[Product Information: template/primer dependence and synthesis direction]{ref}
For a short sequence example, align template $3'\text{-}\mathrm{TACGGA}\text{-}5'$ with primer $5'\text{-}\mathrm{ATG}\text{-}3'$. The primer pairs with the first three template bases. Extension adds C, C and T to its $3'$ end, producing $5'\text{-}\mathrm{ATGCCT}\text{-}3'$. The primer is part of the resulting strand; it is not merely a location marker that disappears when synthesis starts.
The distinction between template and primer is functional. The template specifies the next complementary base; the primer supplies the strand end being extended. A primer may be <DNA> or <RNA> in an appropriate biological or experimental system, but suitability depends on the enzyme and pairing conditions, not simply on calling an oligonucleotide a primer.
In an idealized <polymerase chain reaction> count, two correctly oriented primers permit repeated copying of a bounded target. If each cycle doubles the counted target molecules with no loss, $N_n=N_0 2^n$; ten cycles from one target give $1024$ copies. This is a bookkeeping model, not a measured amplification yield. Failed priming, incomplete extension and competing products violate its assumptions. The original amplification study combined copying with a subsequent restriction-site assay, illustrating that making more material and identifying its sequence are separate experimental tasks.<Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia by R. K. Saiki and others>[1985 abstract: amplification and subsequent restriction-site analysis]{ref}
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