靶向小核RNA基因构建PCR教学实验的生物信息学分析

Bioinformatics Analysis of Establishment of PCR Teaching Experiments Targeting Small Nuclear RNA Genes

摘要: 目的：探讨针对小核RNA基因，构建本科聚合酶链反应(PCR)教学实验的可行性。方法：调取NCBI数据库中小核RNA基因U1、U2、U4、U5及U6的序列，分别截取5’端和3’端部分序列作为上、下游引物，进行电子PCR，分析其靶点情况和引物效率。结果：电子PCR能清楚显示每对引物潜在的靶位点及相应PCR产物的大小。针对U1、U2、U4、U5、U6基因的引物，对应的靶位点数目分别为18、16、4、1、61，对应的PCR产物大小分别为164~166、187~188、144、117、95~108 bp。结论：针对U1、U2、U6基因的引物，其潜在的靶位点数量较多，且绝大部分靶位点的引物结合效率较好，相应的PCR扩增子长度较短，PCR容易实现，PCR连同电泳检测有望在2个小时内完成，比较适合构建本科PCR教学实验。

Abstract: Objective: To establish PCR experiments targeting small nuclear RNA genes, which is expected to be used in undergraduate teaching. Methods: The sequences of snRNA coding genes U1, U2, U4, U5 and U6 in NCBI database were obtained, and the 5’ and 3’ end partial sequences were intercepted as upstream and downstream primers for In-Silico PCR. The targets and primer efficiency were ana-lyzed. Results: The potential target sites of each pair of primers and the size of corresponding PCR products could be clearly displayed by In-Silico PCR. The corresponding target number of primers for U1, U2, U4, U5 and U6 genes were 18, 16, 4, 1, 61, and the corresponding PCR product sizes were 164 - 166, 187 - 188, 144, 117 and 95 - 108 bp. Conclusion: For the primers of U1, U2, U6 gene, there are many potential target binding sites, and most of them have good binding efficiency. The corresponding length of PCR amplicons is short, and the PCR is easy to realize. PCR together with electrophoresis detection is expected to be completed in two hours, which is suitable for the estab-lishment of undergraduate PCR teaching experiment.