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Abstract
DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based
PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP),
remain the most commonly used techniques for methylation mapping. Existing primer
design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based
PCRs due to changes in DNA sequence context caused by bisulfite treatment and many
special constraints both on the primers and the region to be amplified for such experiments.
Therefore, the present study was designed to develop a program for such applications.
MethPrimer, based on Primer 3, is a program for designing PCR primers for methylation
mapping. It first takes a DNA sequence as its input and searches the sequence for
potential CpG islands. Primers are then picked around the predicted CpG islands or
around regions specified by users. MethPrimer can design primers for BSP and MSP.
Results of primer selection are delivered through a web browser in text and in graphic
view.