Li Long-Cheng, Dahiya Rajvir
Department of Urology, Veterans Affairs Medical Center, and University of California San Francisco, San Francisco, CA 94121, USA.
Bioinformatics. 2002 Nov;18(11):1427-31. doi: 10.1093/bioinformatics/18.11.1427.
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.
DNA甲基化是一种基因调控的表观遗传机制。基于亚硫酸氢盐转化的PCR方法，如亚硫酸氢盐测序PCR（BSP）和甲基化特异性PCR（MSP），仍然是甲基化图谱绘制最常用的技术。由于亚硫酸氢盐处理导致DNA序列背景的变化以及此类实验对引物和待扩增区域的许多特殊限制，为标准PCR开发的现有引物设计程序无法处理基于亚硫酸氢盐转化的PCR的引物设计。因此，本研究旨在开发一个适用于此类应用的程序。
基于Primer 3的MethPrimer是一个用于设计甲基化图谱绘制PCR引物的程序。它首先将DNA序列作为输入，并在序列中搜索潜在的CpG岛。然后在预测的CpG岛周围或用户指定的区域周围挑选引物。MethPrimer可以为BSP和MSP设计引物。引物选择结果通过网页浏览器以文本和图形视图呈现。
