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Target Identification and Validation in Drug Discovery pp 59–71Cite as

siRNA Design Principles and Off-Target Effects

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 986))

Abstract

Short interfering RNAs (siRNAs) are a major research tool that allows for knock-down of target genes via selective mRNA destruction in almost all eukaryotic organisms. siRNAs typically consist of a synthetic ∼21 nucleotide (nt) RNA-duplex where one strand is designed with perfect complementarity to the target mRNA. Although siRNAs were initially thought to be very target-specific because of their design, it turned out during the last years that all siRNAs have a more or less pronounced intrinsic off-target activity which can make the interpretation of data from siRNA experiments difficult. Here we describe essential rules for siRNA design that should be taken into account in order to obtain potent siRNAs with minimal off-target activity. In addition, we describe how to control for off-target activity in siRNA experiments.

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Acknowledgments

Our research is supported in part by the BMBF (NGFN+, FKZ PIM-01GS0804-5 to G.M.), the Bavarian Genome Research Network (BayGene to G.M.), the Deutsche Forschungsgemein­schaft (DFG), and Roche Kulmbach GmbH. S.P. received a fellowship from the Roche Postdoc Fellowship Program.

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Authors and Affiliations

  1. Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany

    Sebastian Petri & Gunter Meister

Authors
  1. Sebastian Petri
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  2. Gunter Meister
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Editor information

Editors and Affiliations

  1. Director, Department of Pharmacology, Boehringer Ingelheim RCV GmbH & Co KG, N/A, Vienna, N/A, Austria

    Jurgen Moll

  2. Project and Team Leader, Cell Biology, Nerviano Medical Sciences, Viale Pasteur 10, Nerviano, 20014, Milano, Italy

    Riccardo Colombo

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Petri, S., Meister, G. (2013). siRNA Design Principles and Off-Target Effects. In: Moll, J., Colombo, R. (eds) Target Identification and Validation in Drug Discovery. Methods in Molecular Biology, vol 986. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-311-4_4

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  • DOI: https://doi.org/10.1007/978-1-62703-311-4_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-310-7

  • Online ISBN: 978-1-62703-311-4

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