Letter abstract
Nature Biotechnology 26, 578 - 583 (2008)
Published online: 27 April 2008 | doi:10.1038/nbt1404
The impact of target site accessibility on the design of effective siRNAs
Hakim Tafer1,5, Stefan L Ameres2,4,5, Gregor Obernosterer3,5, Christoph A Gebeshuber3, Renée Schroeder2, Javier Martinez3 & Ivo L Hofacker1
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.
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Institute of Theoretical Biochemistry (TBI), University of Vienna, Währingerstra
e 17, 1090 Vienna, Austria. - Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
- Present address: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605-2324, USA.
- These authors contributed equally to this work.
Correspondence to: Ivo L Hofacker1 e-mail: ivo@tbi.univie.ac.at
Correspondence to: Javier Martinez3 e-mail: javier.martinez@imba.oeaw.ac.at
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