What is degenerate PCR?
Degenerate PCR is in most respect identical to ordinary PCR, but with one major difference. Instead of using specific PCR primers with a given sequence, you use mixed PCR primers. That is, if you do not know exactly the sequence of the gene you are going to amplify, you insert ‘wobbles’ in the PCR primers where there is more than one possibility. For instance if you just have a protein motif, you can back-translate the protein motif to the corresponding nucleotide motif. (Protein –> DNA Sequence). Example of a degenerate PCR primer designed after a protein motif. Trp Asp Thr Ala Gly Gln Glu 5′ TGG GAY ACN GCN GGN CAR GA 3′ This gives a mix of 256 different oligonucleotides. Where the Y=C or T, R=G or A, N=G, A, T or C. The more wobbles you introduce in the PCR primer the more degenerate it gets. (The degeneracy of the primer is produced during DNA synthesis, you do not need to order 256 different primers to get a 256 mix, that’s a lot of paper work!! and expensive). Degenerate nucleot
