Editing Primer (molecular biology) (section)

===Degenerate primers===
{{main|Degenerate bases}}
Some situations may call for the use of ''degenerate primers.'' These are mixtures of primers that are similar, but not identical. These may be convenient when amplifying the same [[gene]] from different [[organism]]s, as the sequences are probably similar but not identical. This technique is useful because the [[genetic code]] itself is [[Degenerate code|degenerate]], meaning several different [[codon]]s can code for the same [[amino acid]]. This allows different organisms to have a significantly different genetic sequence that code for a highly similar protein. For this reason, degenerate primers are also used when primer design is based on [[protein sequence]], as the specific sequence of codons are not known. Therefore, primer sequence corresponding to the [[amino acid]] [[isoleucine]] might be "ATH", where A stands for [[adenine]], T for [[thymine]], and H for [[adenine]], [[thymine]], or [[cytosine]], according to the [[genetic code]] for each [[codon]], using the IUPAC symbols for [[degenerate bases]]. Degenerate primers may not perfectly hybridize with a target sequence, which can greatly reduce the specificity of the PCR amplification.

''Degenerate primers'' are widely used and extremely useful in the field of [[microbial ecology]]. They allow for the amplification of genes from thus far uncultivated [[microorganism]]s or allow the recovery of genes from organisms where genomic information is not available. Usually, degenerate primers are designed by aligning gene sequencing found in [[GenBank]]. Differences among sequences are accounted for by using IUPAC degeneracies for individual bases. PCR primers are then synthesized as a mixture of primers corresponding to all permutations of the codon sequence.