【分享】一篇关于简并引物设计的经典文献CODEHOP
丁香园论坛
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文章题目：Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences
Nucleic Acids Research, 1998 Apr 1; 26(7):1628-1635.
设计兼并引物的方法很多，但你听说过如何降低兼并度，以及如何提高成功率的方法吗？CODEHOP方法肯定是一篇这方面的精典文章！推荐出来，与大家共享！
摘要：
We describe a new primer design strategy for PCR amplification ofunknown targets that are related to multiply-aligned protein sequences.Each primer consists of a short 3' degenerate core region and a longer5' consensus clamp region. Only 3-4 highly conserved amino acidresidues are necessary for design of the core, which is stabilized bythe clamp during annealing to template molecules. During later roundsof amplification, the non-degenerate clamp permits stable annealing toproduct molecules. We demonstrate the practical utility of this hybridprimer method by detection of diverse reverse transcriptase-like genesin a human genome, and by detection of C5 DNA methyltransferasehomologs in various plant DNAs. In each case, amplified products weresufficiently pure to be cloned without gel fractionation. ThisCOnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategyhas been implemented as a computer program that is accessible over theWorld-Wide Web (http://blocks.fhcrc.org/codehop.html)and is directly linked from the BlockMaker multiple sequence alignmentsite for hybrid primer prediction beginning with a set of relatedprotein sequences.
Nucleic Acids Research, 1998 Apr 1; 26(7):1628-1635.
设计兼并引物的方法很多，但你听说过如何降低兼并度，以及如何提高成功率的方法吗？CODEHOP方法肯定是一篇这方面的精典文章！推荐出来，与大家共享！
摘要：
We describe a new primer design strategy for PCR amplification ofunknown targets that are related to multiply-aligned protein sequences.Each primer consists of a short 3' degenerate core region and a longer5' consensus clamp region. Only 3-4 highly conserved amino acidresidues are necessary for design of the core, which is stabilized bythe clamp during annealing to template molecules. During later roundsof amplification, the non-degenerate clamp permits stable annealing toproduct molecules. We demonstrate the practical utility of this hybridprimer method by detection of diverse reverse transcriptase-like genesin a human genome, and by detection of C5 DNA methyltransferasehomologs in various plant DNAs. In each case, amplified products weresufficiently pure to be cloned without gel fractionation. ThisCOnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategyhas been implemented as a computer program that is accessible over theWorld-Wide Web (http://blocks.fhcrc.org/codehop.html)and is directly linked from the BlockMaker multiple sequence alignmentsite for hybrid primer prediction beginning with a set of relatedprotein sequences.
