Two reverse primer sequences for a single forward primer - (Jul/09/2012 )
I have a small doubt. Please help me out.
In one research paper, I have found a forward primer sequence with "R" in one of its positions. which means that it could be either A or G. This primer serves as a common forward primer for two genes. In this research paper, they have given two reverse primer sequences for each of the gene. Please see below:
P1: HLA-C forward(common): 5'-GCC GCG AGT CCR AGA GG-3'
P2: HLA-C1 reverse 5'-GCG CAG GTT CCG CAG GC-3'
P3: HLA-C1 reverse 5'-GTT GTA GTA GCC GCG CAG G-3
P4: HLA-C2 reverse 5'-CGC GCA GTT TCC GCA GGT-3'
P5: HLA-C2 reverse 5'-GTT GTA GTA GCC GCG CAG T-3'
It was also mentioned in the research article that "Two reactions were used to amplify both C1 and C2."
My doubt here is why they have given two reverse primer sequences for a single gene? Can we use any one of the reverse primer sequences for my PCR reaction? Please help me out. Eagerly awaiting for the response.
It sounds like there are isoforms of the gene - the different reverse primers will give you the different forms.