we are looking for 2 primer-pairs for nested PCR and subsequent sequencing of bisulfit-treated DNA. In case of primers with internal CpG dinucleotides, we have to design a mix of primers with C or T at the corresponding position. But what about the other C-residues within the primer sequence? Petronis et al. (Schizophr Bull 29:169ff (2003)) found in their study some methylated C-residues, which are not in CpG or CpNpG. Isn't there the danger of loosing templates and shifting of results?
Is there anybody who has experience with this problem?
mC not in CpG? Primer selection
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