CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design
CODEHOP (COnsensus-DEgenerate hybrid oligonucleotide primer) PCR primer design
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DOI：
10.1093/nar/gkg524
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Henikoff, S
中科院分区：
文献类型：
--
作者：
Rose, TM;Henikoff, JG;Henikoff, S
我们开发了一种新的引物设计策略，用于PCR扩增远缘基因序列的基础上的共识简并杂交寡核苷酸引物（CODEHOPs）。已编写了一个交互式程序，用于从多重比对蛋白质序列中的保守氨基酸块设计CODEHOP PCR引物。每个CODEHOP由相关引物库组成，所述引物库含有编码3'简并核心内的3-4个高度保守氨基酸的所有可能的核苷酸序列。较长的5'非简并夹区域含有针对每个侧翼密码子预测的最可能的核苷酸。在PCR扩增中使用CODEHOP以分离编码保守氨基酸序列的远缘相关序列。引物设计软件和CODEHOP PCR策略已被用于鉴定和表征不同植物、动物和细菌物种中的新基因直系同源物和旁系同源物。此外，这种方法在鉴定新的病原体物种方面也取得了成功。CODEHOP设计器（http：blocks.fhcrc.org）链接到块数据库万维网（http：//blocks.fhcrc.org）内的块制造器和多对齐处理器。
We have developed a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). An interactive program has been written to design CODEHOP PCR primers from conserved blocks of amino acids within multiply-aligned protein sequences. Each CODEHOP consists of a pool of related primers containing all possible nucleotide sequences encoding 3-4 highly conserved amino acids within a 3' degenerate core. A longer 5' non-degenerate clamp region contains the most probable nucleotide predicted for each flanking codon. CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence. The primer design software and the CODEHOP PCR strategy have been utilized for the identification and characterization of new gene orthologs and paralogs in different plant, animal and bacterial species. In addition, this approach has been successful in identifying new pathogen species. The CODEHOP designer (http://blocks.fhcrc.org/codehop.html) is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org).