Fig. 1

PCR primers for CDKN2B and DAPK1. a CpG dinucleotides are shown in red, and the position matching the cytosine in the dinucleotide is underlined (C in forward primers and G in reverse). Blue thymines (forward primers) and adenines (reverse primers) match cytosines in the DNA sequence that are not part of CpG dinucleotides and therefore undergo bisulfite modification. b Each of the six primer types tested are shown. The letters in red indicate the substitution in the forward primer using IUPAC nomenclature. The flanking Ns denote the flanking sequence. For the mismatch primer (with a mismatched base), the base was arbitrarily chosen as an A in the forward primer (and a T in the reverse primer). In the primer with the abasic site, there is no base attached to the deoxyribose while the regular DNA backbone is intact