Designing PCR Primer for DNA Methylation Mapping

DNA methylation is an epigenetic mechanism of gene regulation, and aberrant methylation has been associated with various types of diseases, especially cancers. Detection of DNA methylation has thus become an important approach for studying gene regulation and has potential diagnostic application. Bisulfite-conversion-based PCR methods, such as bisulfite-sequencing PCR (BSP) and methylation-specific PCR (MSP), remain the most commonly used techniques for methylation detection. Primer design for this type of PCR is challenging because of the extreme DNA sequence composition after bisulfite modification and the special constraints on the primers and their location on the DNA template. To facilitate methylation detection, a primer design program called MethPrimer has been developed specifically for bisulfite-conversion-based PCR. MethPrimer accepts a DNA sequence as input, performs a digital bisulfite conversion of the input sequence, and then picks primers on the converted sequence. Results of primer selection are delivered through a Web browser in text and graphic views. This chapter discusses the process of using MethPrimer to design BSP and MSP primers.