Figure 6-9: Correct base-pairing at the 3' end of PCR primers is the basis of allele-specific PCR.

The allele-specific oligonucleotide primers ASP1 and ASP2 are designed to be identical to the sequence of the two alleles over a region preceding the position of the variant nucleotide, up to and terminating in the variant nucleotide itself. ASP1 will bind perfectly to the complementary strand of the allele 1 sequence permitting aplification with conserved primer. However, the 3'-terminal C of the ASP2 primer mismatches with the T of the allele 1 sequence, making almplification impossible. Similarly ASP2 can bind perfectly to allele 2 and initiate amplification, unlike ASP1.