摘要
目的从引物设计的合理性、扩增片段的保守性、检出目的片段的敏感性等方面比较4对猴空泡病毒40(SV40)核酸检测引物之间的差异,为寻找保守性好、稳定高效的SV40核酸序列检测法提供理论基础。方法以目前已知的23个不同SV40毒株完全基因组为基础数据,用DNAMAN6.0.40软件对4对引物及其扩增片段的保守性进行分析;用clust-alX1.83软件对23个SV40基因组序列进行多重序列对齐分析;用TreeView1.6.6软件构建系统进化树;用Oligo6.71软件对4对引物的特性进行分析。结果对于接受号为DQ218418病毒株而言,4对引物的序列均不保守;对于接受号为J02400、NC_001669、AF316139和AF316141的4个病毒株而言,引物对GCVp1和GCT的序列是保守的;对于除了DQ218418之外的病毒株而言,引物对VP1的序列是保守的;对于除了DQ218418、AF180737之外的病毒株而言,引物对T的序列是保守的。结论目前通用的SV40核酸检测引物针对的SV40病毒株只有4个,本室合成的检测引物针对的病毒株有21个;本室设计的SV40检测引物和通用引物相比具有保守性好、适用性广、参数理想等优点;对于某些高度变异的毒株,应单独进行引物设计。
Objective To compare the reasonability of design, conservation of amplified gene fragments and sensitivity in detection of target gene fragment of four pairs of PCR primers for simian vacuolating virus 40 （ SV40 ） DNA and provide theoretical basis for stable and effective method for SV40 DNA sequencing. Methods Four pairs of PCR primers and the conservation of amplified gene fragments were analyzed by DNAMAN 6. 0. 40 software based on known genomes of 23 different SV40 strains. Multiple sequence alignment was carried out by clustalX1.83 software. Phylogenetic tree was constructed by TreeViewl. 6. 6 software. The characteristics of the four pairs of primers were analyzed by Oligo 6.71 software. Results All the sequences of four pairs of primers were not conservative for the SV40 strain with an accession number of DQ218418. The GCVpl and GCT sequences of primers were conservative for four SV40 strains with accession numbers of J02400,NC_001669,AF316139 and AF316141. The VP1 sequences of primers were conservative for the SV40 strains except DQ218418. The T sequences of primers were conservative for the SV40 strains except DQ218418 and AF180737. Conclusion The synthetic primers were specific to 21 SV40 strains. Compared with common primers ,the synthetic primers were of good conservation,wide adaptivity and ideal parameters. Specific primers shall be designed for highly variant SV40 strains.
出处
《中国生物制品学杂志》
CAS
CSCD
2007年第6期409-412,共4页
Chinese Journal of Biologicals
