Rational siRNA design for RNA interference
Rational siRNA design for RNA interference
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DOI：
10.1038/nbt936
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发表时间：
2004-03-01
影响因子：
46.9
通讯作者：
Khvorova, A
中科院分区：
文献类型：
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作者：
Reynolds, A;Leake, D;Khvorova, A
短干扰RNA通过高度调节的酶介导的过程抑制基因表达，称为RNA干扰（RNAi）1-4。RNAi涉及多个RNA-蛋白质相互作用，其特征在于四个主要步骤：siRNA与RNA诱导的沉默复合物（RISC）的组装、RISC的激活、靶标识别和靶标切割。这些相互作用可以在siRNA-RISC组装和活化期间偏向链选择，并有助于RNAi的总体效率5，6。为了鉴定可能有助于每个步骤有效加工的siRNA特异性特征，我们对靶向两个基因mRNA的180种siRNA进行了系统分析。鉴定了与siRNA功能性相关的八个特征：低G/C含量、在有义链3 '末端偏向低内部稳定性、缺乏反向重复序列和有义链碱基偏好（位置3、10、13和19）。进一步的分析显示，应用包含所有八个标准的算法显著提高了有效的siRNA选择。这突出了合理设计用于选择有效siRNA和促进功能基因敲除研究的效用。
Short-interfering RNAs suppress gene expression through a highly regulated enzyme-mediated process called RNA interference (RNAi) 1-4. RNAi involves multiple RNA-protein interactions characterized by four major steps: assembly of siRNA with the RNA-induced silencing complex (RISC), activation of the RISC, target recognition and target cleavage. These interactions may bias strand selection during siRNA-RISC assembly and activation, and contribute to the overall efficiency of RNAi 5,6. To identify siRNA-specific features likely to contribute to efficient processing at each step, we performed a systematic analysis of 180 siRNAs targeting the mRNA of two genes. Eight characteristics associated with siRNA functionality were identified: low G/C content, a bias towards low internal stability at the sense strand 3'-terminus, lack of inverted repeats, and sense strand base preferences (positions 3, 10, 13 and 19). Further analyses revealed that application of an algorithm incorporating all eight criteria significantly improves potent siRNA selection. This highlights the utility of rational design for selecting potent siRNAs and facilitating functional gene knockdown studies.