Bradác Ivan, Svobodová Vareková Radka, Wacenovsky Michael, Skrdla Michal, Plchút Martin, Polcík Martin
Bioinformatics group, ANF DATA (subsidiary of Siemens), Herspická 5, 639 00 Brno, Czech Republic.
Biochem Biophys Res Commun. 2007 Jul 20;359(1):83-7. doi: 10.1016/j.bbrc.2007.05.056. Epub 2007 May 21.
RNA interference is a powerful tool for gene silencing, which is mediated by introducing siRNA. In the present study, statistical analyses of published siRNA selection criteria, the interpretation of some criteria and systematic searching for new criteria have been carried out for CGB siRNA and siRecords databases. The results of the analyses are as follows: (i) Our study supports the two-state model of the RNA-induced silencing complex (RISC). (ii) Stable 5'-S ends of a siRNA sequence, higher stability of the whole siRNA, and low breaking energy of siRNA duplex occurs in effective siRNA sequences. Also low internal stability of the 5'-AS terminus is preferred. (iii) Secondary structure can be successfully used as an RNAi selection criterion. (iv) Several published sequence criteria have been confirmed and also new criteria have been developed. (v) Also a Target Patterns criterion, which is comparable or better than the best known criteria, has been created.
RNA干扰是一种通过引入小干扰RNA（siRNA）介导的强大的基因沉默工具。在本研究中，针对CGB siRNA和siRecords数据库，对已发表的siRNA选择标准进行了统计分析、对一些标准进行了解读并系统地寻找新的标准。分析结果如下：（i）我们的研究支持RNA诱导沉默复合体（RISC）的双态模型。（ii）有效siRNA序列中存在siRNA序列稳定的5'-S末端、整个siRNA更高的稳定性以及siRNA双链体的低断裂能。5'-AS末端的内部稳定性也较低为优。（iii）二级结构可成功用作RNA干扰的选择标准。（iv）一些已发表的序列标准得到了证实，同时也制定了新的标准。（v）还创建了一种目标模式标准，其与最知名的标准相当或更好。
