Method for optimizing methylation-specific PCR

The methylation of the CpG islands that are associated with the promoters of numerous genes can be associated with gene silencing. Therefore, it is an important area of research, and several techniques have been developed for the rapid and sensitive analysis of methylation. One of these methods is methylation-specific PCR (1). Most commonly, the PCR conditions are optimized using DNA prepared from cell lines that have a relatively homogeneous methylation pattern. However, in the typical tissue specimen, there will be a mixture of cells, with a number of patterns of methylation. We report that the optimization steps, which are appropriate when working with DNA prepared from cell populations with uniform methylation patterns, are not appropriate when analyzing DNA from tissues