用于聚合酶链式反应(PCR)引物设计的计算机程序

 本文报道了两个用于PCR引物设计的计算机程序PCRDESN和PCRDESNA。PCRDESN程序主要从以下4个方面评价用户自己设计的一对引物的质量:(1)引物内的碱基反向重复或发夹结构,(2)两个引物之间的碱基互补配对,(3)两个引物之间的同源性,(4)引物的碱基组成及特点和T_m值计算。通过用多例文献发表的及本院有关实验室提供的引物对序列的验证,确定了程序的运算参数,证明该程序能较好地检验引物对的质量和解释某些PCR实验失败的原因。PCRDESNA程序采用逐级优化的方法和比PCRDESN所选用的更严紧的引物选择参数对用户提供的核酸序列进行快速检索,以确定所有可能的和合适的引物对。

Computer Programs for Polymerase Chain Reaction (PCR) Primer Design

We have developed two computer programs for PCR primer design.The PCRDESN program evaluates the quality of a primer set based on the 4 criteria as follow, (1) inverted repeated (or haipin strcture) within each of the two primers, (2) complementary between the primer set, (3) homology between the primer set, and (4) the composition and feature of the sequences and calculation of Tm value.Tested by a number of sequences of primer sets published or provided by some related laboratories, the parameters of the program algorithm were determined.It is proved that PCRDESN can examine the quality of primer sets properly and give good explanations for the failure of some PCR experiments.The PCRDESNA program, using a step-by-step optimization method and more stringent parameters than those used by PCRDESN, may rapidly scan nucleic acid sequences provided by the user to select all possible pairs of oligonucleotides that are suitable for acting as PCR primers.