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MPprimer: a program for reliable multiplex PCR primer design

热5 quwubin 添加于 2010-4-8 18:25 | 2782 次阅读 | 0 个评论

作者
Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Hang X, Wang X, Zhao D, Zhang C
摘要
Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility. A program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2x to 5x plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy), which has 79 exons, for 20x, 20x, 20x, 14x, and 5x plex PCR reactions in five tubes to detect underlying exon deletions. MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.
详细资料
- 文献种类: Journal Article
- 期刊名称: BMC Bioinformatics
- 期卷页: 2010年第11卷第1期 143页
- 日期: 2010
- ISBN: 1471-2105
学科领域生物医药 » 生物学
标签

Multiplex PCR
相关链接 DOI URL
附件
MPprimer: a program for reliable multiplex PCR primer design

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【原创】

这是自己的工作。

MPprimer：一个设计高可信度多重PCR引物的软件. 它基于被广泛应用的引物设计软件Primer3 (Whitehead Institute)和多因素引物特异性评估系统MFEprimer (张成岗实验室，北京放射与辐射医学研究所)而设计，因而可以设计出高质量且又高特异性的多重PCR引物组合，同时合理规划多重PCR产物分子量，以免影响电泳条的分辨，并且排除了引物二聚体（dimer）的形成，最后MPprimer将生成虚拟的电泳条带以帮助用户选择更好的引物组合。

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