Development of a software tool and criteria evaluation for efficient design of small interfering RNA
Development of a software tool and criteria evaluation for efficient design of small interfering RNA
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DOI：
10.1016/j.bbrc.2010.11.114
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发表时间：
2011-01-07
影响因子：
3.1
通讯作者：
Garg, Sanjeev
中科院分区：
文献类型：
--
作者：
Chaudhary, Aparna;Srivastava, Sonam;Garg, Sanjeev
RNA干扰可以作为小干扰RNA （small interfering RNA, siRNA）介导的基因沉默工具。有效和特异性RNAi加工的关键步骤是选择合适的构建体。主要设计标准，即雷诺兹设计规则，热力学稳定性，内部重复，免疫刺激基序被强调并在siRNA设计工具中实现。该工具提供热力学稳定性评分。GC内容和基于输出中其他设计标准的总分。用不同的数据集建立了该工具的可行性。总的来说，该工具生成的siRNA结构具有更好的热力学分数和位置性质。使用现有工具可以观察到相当的热力学分数和更好的总分。此外，产生的结果具有可比的脱靶沉默效果。在WEKA中实现了附加标准的标准评估。(C) 2010爱思唯尔公司版权所有。
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. (C) 2010 Elsevier Inc. All rights reserved.