Blich gene of B. licheniformis (F 5′-AKACGGAAGTGACGGGAAC-3′ and R 5′-AGAAACTTTTCRAGCGCTT-3′)
Hi Dan,
these are degenerated primers. R stands for either A or G, and K stands for either G or T.
Best
Soner
Degenerate primers are a mix of oligonucleotide sequences in which some positions contain a number of possible bases, giving a population of primers with similar sequences that cover all possible nucleotide combinations for a given DNA sequence. The primers you mentioned to amplify Blich gene from Bacillus licheniformis were designed to tolerate any sequence variability in the primer's binding sites. May be the gene sequence is variable among isolates within Bacillus licheniformis, for this reason the primers designed with R or K at certain positions. K (from Keto) could be G or T and R (from puRine) could be A or G.
Regards
Mohamed
To cover a large diversified spectrum of genetic variants, we use to opt for degenerate bases (R = A,G ; Y = C,T; M = A,C ; K = G,T; S =C,G; W = A,T; H = A,C,T ; B = C,G,T ; V = A,C,G ; D = A,G,T; N = A,C,G,T) giving us a set of mixed primers alloxing to increase the genetic matching chance.
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