Designing PCR primer for DNA methylation mapping.
Designing PCR primer for DNA methylation mapping.
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DOI：
10.1007/978-1-59745-528-2_19
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发表时间：
2007
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--
通讯作者：
Long-Cheng Li
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文献类型：
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作者：
Long-Cheng Li
DNA甲基化是基因调控的表观遗传机制，异常甲基化与多种疾病，尤其是癌症有关。因此，DNA甲基化检测已成为研究基因调控的重要方法，并具有潜在的诊断应用价值。基于亚硫酸氢盐转化的 PCR 方法，例如亚硫酸氢盐测序 PCR (BSP) 和甲基化特异性 PCR (MSP)，仍然是最常用的甲基化检测技术。由于亚硫酸氢盐修饰后 DNA 序列组成极端，并且引物及其在 DNA 模板上的位置受到特殊限制，因此此类 PCR 的引物设计具有挑战性。为了促进甲基化检测，专门为基于亚硫酸氢盐转化的 PCR 开发了名为 MethPrimer 的引物设计程序。 MethPrimer 接受 DNA 序列作为输入，对输入序列进行数字亚硫酸氢盐转换，然后在转换后的序列上挑选引物。引物选择的结果通过网络浏览器以文本和图形视图形式提供。本章讨论使用 MethPrimer 设计 BSP 和 MSP 引物的过程。
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.