Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1186/1471-2105-11-143 | BMC Bioinformatics |
Keywords | Field | DocType |
electrophoretic mobility,microarrays,greedy algorithm,multiplex pcr,polymerase chain reaction,dna primers,bioinformatics,algorithms,microbiology,genomics | In silico PCR,Polymerase chain reaction,Multiplex polymerase chain reaction,Biology,Amplicon,Primer (molecular biology),Bioinformatics,Multiplex ligation-dependent probe amplification,Genetics,Primer dimer,DNA microarray | Journal |
Volume | Issue | ISSN |
11 | 1 | 1471-2105 |
Citations | PageRank | References |
15 | 0.57 | 10 |
Authors | ||
10 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zhiyong Shen | 1 | 112 | 12.08 |
| Wubin Qu | 2 | 42 | 3.66 |
| Wen Wang | 3 | 15 | 0.57 |
| Yiming Lu | 4 | 96 | 7.65 |
| Yonghong Wu | 5 | 15 | 0.57 |
| ZhiFeng Li | 6 | 1073 | 55.45 |
| Xingyi Hang | 7 | 31 | 1.28 |
| Xiaolei Wang | 8 | 16 | 2.94 |
| Dongsheng Zhao | 9 | 64 | 6.88 |
| Chenggang Zhang | 10 | 77 | 5.13 |