Hairpin-Bisulfite Polymerase Chain Reaction PCR
Laird C. et al, published a great paper describing this method that they utilized to assess the fidelity of methylation transmission of CpG islands within the FMR1 gene of human lymphocytes. They generated a hairpin-linker with staggered ends (25 base pairs long), complementary to the targeted cut-site of the DNA, which was used after restriction enzyme digest of the DNA. The linker was attached to the DNA through the use of DNA ligase. The double-stranded target DNA was then subjected to sodium bisulfite treatment, and PCR amplification with designed primers that bound to the linker approximately 200 nucleotides away. The PCR products were then subsequently sequenced.
C. Laird et al. Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc Nat Acad Sci (2004) 101: 204-209.