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Designing Optimal siRNA Based on Target Site Accessibility

  • Ivo L. Hofacker
  • Hakim Tafer
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 623)

Abstract

RNA interference, mediated by small interfering RNAs (siRNAs), is a powerful tool for investigation of gene functions and it is increasingly being used as a therapeutic agent. However, not all siRNAs are equally potent - although simple rules for the selection of good siRNAs were proposed early on, siRNAs are still plagued with widely fluctuating efficiency. Recently, new design tools that incorporate both the structural features of the targeted RNAs and the sequence features of the siRNAs have substantially improved the efficacy of siRNAs. In this chapter, we present the algorithms behind these accessibility-aided tools and show how to design efficient siRNAs with their help.

Key words

RNA interference mRNA structure Target accessibility siRNA design tools Tutorial 

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Institute for Theoretical ChemistryUniversity ViennaViennaAustria

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