Department of Chemical Engineering, IIT Kanpur, UP 208 016, India.
Biochem Biophys Res Commun. 2011 Jan 7;404(1):313-20. doi: 10.1016/j.bbrc.2010.11.114. Epub 2010 Dec 8.
RNA interference can be used as a tool for gene silencing mediated by small interfering RNAs (siRNA). The critical step in effective and specific RNAi processing is the selection of suitable constructs. Major design criteria, i.e., Reynolds's design rules, thermodynamic stability, internal repeats, immunostimulatory motifs were emphasized and implemented in the siRNA design tool. The tool provides thermodynamic stability score, GC content and a total score based on other design criteria in the output. The viability of the tool was established with different datasets. In general, the siRNA constructs produced by the tool had better thermodynamic score and positional properties. Comparable thermodynamic scores and better total scores were observed with the existing tools. Moreover, the results generated had comparable off-target silencing effect. Criteria evaluations with additional criteria were achieved in WEKA.
RNA 干扰可用作由小干扰 RNA (siRNA) 介导的基因沉默的工具。有效且特异性的 RNAi 处理的关键步骤是选择合适的构建体。主要设计标准，即 Reynolds 设计规则、热力学稳定性、内部重复、免疫刺激基序，在 siRNA 设计工具中得到了强调和实施。该工具提供热力学稳定性评分、GC 含量和基于其他设计标准的总分。该工具的可行性已通过不同的数据集建立。一般来说，该工具生成的 siRNA 构建体具有更好的热力学评分和位置特性。与现有的工具相比，观察到可比的热力学评分和更好的总分。此外，所产生的结果具有可比的脱靶沉默效果。在 WEKA 中使用其他标准实现了标准评估。
