The impact of target site accessibility on the design of effective siRNAs

Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activat...

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Bibliographic Details
Published in:Nature biotechnology 2008-05, Vol.26 (5), p.578-583
Main Authors: Obernosterer, Gregor, Hofacker, Ivo L, Tafer, Hakim, Ameres, Stefan L, Gebeshuber, Christoph A, Schroeder, Renée, Martinez, Javier
Format: Article
Language:English
Subjects:
Agriculture
Base Sequence
Binding Sites
Bioinformatics
Biological and medical sciences
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Calibration
Computer Simulation
Design
Drug Design
Evaluation
Fundamental and applied biological sciences. Psychology
Gene Targeting - methods
Genetic engineering
Genetic research
letter
Life Sciences
Models, Chemical
Models, Genetic
Molecular Sequence Data
Nucleotides
Properties
Ribonucleic acid
RNA
RNA Interference
RNA, Small Interfering - genetics
Sequence Analysis, RNA - methods
Structure
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Summary:Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.
ISSN:1087-0156
1546-1696
DOI:10.1038/nbt1404