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The impact of target site accessibility on the design of effective siRNAs - Nature Biotechnology

  • ️Hofacker, Ivo L
  • ️Sun Apr 27 2008
  • Letter
  • Published: 27 April 2008

Nature Biotechnology volume 26, pages 578–583 (2008)Cite this article

Abstract

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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Acknowledgements

We would like to thank A. Khvorova for critical discussions during the project as well as Dharmacon Inc. for providing siRNA knockdown data. H.T. is supported by Siemens and the Wiener Wissenschafts-, Technologie-, und Forschungsfonds. S.L.A. is funded by the Austrian Science Fund FWF through WK001. J.M. is a Junior Group Leader at IMBA, the Institute of Molecular Biotechnology supported by the Austrian Academy of Sciences. Funding by the Austrian Government's GEN-AU is acknowledged by R.S., J.M. and I.L.H. We thank the members of the Hofacker, Schroeder and Martinez labs for encouragement, helpful discussions and comments on the manuscript.

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Author notes

  1. Stefan L Ameres

    Present address: Present address: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605-2324, USA.,

  2. Hakim Tafer, Stefan L Ameres and Gregor Obernosterer: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Theoretical Biochemistry (TBI), University of Vienna, Währingerstraße 17, Vienna, 1090, Austria

    Hakim Tafer & Ivo L Hofacker

  2. Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr-Gasse 9/5, Vienna, 1030, Austria

    Stefan L Ameres & Renée Schroeder

  3. Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Dr. Bohr-Gasse 3, Vienna, 1030, Austria

    Gregor Obernosterer, Christoph A Gebeshuber & Javier Martinez

Authors

  1. Hakim Tafer

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  2. Stefan L Ameres

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  3. Gregor Obernosterer

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  4. Christoph A Gebeshuber

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  5. Renée Schroeder

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  6. Javier Martinez

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  7. Ivo L Hofacker

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Contributions

H.T., S.L.A. and G.O. initiated research, designed and performed the experiments and analyzed data. I.L.H. designed algorithms, supervised implementation and analysis. C.A.G. performed western blot analysis. R.S. supervised experimental work and analysis. J.M. supervised experimental work and analysis and procured access to the Dharmacon data. All authors contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Javier Martinez or Ivo L Hofacker.

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Tafer, H., Ameres, S., Obernosterer, G. et al. The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26, 578–583 (2008). https://doi.org/10.1038/nbt1404

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  • Received: 21 December 2007

  • Accepted: 07 April 2008

  • Published: 27 April 2008

  • Issue Date: May 2008

  • DOI: https://doi.org/10.1038/nbt1404