This method combines sodium bisulfite treatment of DNA and PCR single strand conformation polymorphism to reveal DNA methylation patterns. Primers are designed to anneal to the bisulfite-converted sequences that have no CpG sites in the corresponding region of the native DNA state. SSCP is then used to reveal any differences between amplified products from methylated and unmethylated DNA. This method is great, and can easily study the DNA methylation very simply. Moreover, quantitative data can be obtained. Unfortunately, sometimes, SSCP can produce more than two bands or a smearing pattern that will complicate result interpretation. It is therefore important to optimize a protocol before proceeding.
Maekawa et al. DNA methylation analysis using bisulfite treatment and PCR-Single-Strand conformation polymorphism in colorectal cancer showing microsatellite instability. Biochem Biophys Res Commun (1999) 262: 671-676.