Primer (molecular biology)

A 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 $3^{\prime }$ 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.^[ref]

For a short sequence example, align template $3^{\prime }\text{-}\mathrm{TACGGA}\text{-}{5}^{\prime }$ with primer $5^{\prime }\text{-}\mathrm{ATG}\text{-}{3}^{\prime }$. The primer pairs with the first three template bases. Extension adds C, C and T to its $3^{\prime }$ end, producing $5^{\prime }\text{-}\mathrm{ATGCCT}\text{-}{3}^{\prime }$. 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.^[ref]