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Designing Functional siRNA with Reduced Off-Target Effects

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siRNA Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 942))

Abstract

RNA interference (RNAi) mediated by small interfering RNA (siRNA) is now widely used to knock down gene expression in a sequence-specific manner, making it a powerful tool not only for studying gene functions but also for therapeutic applications. siRNA decreases the expression level of the intended target gene with complete complementarity by cleaving its mRNA. However, the efficacy of each siRNA widely varies depending on its sequence in mammalian cells; only a limited fraction of randomly designed siRNAs is functional. Moreover, off-target silencing effects arise when the siRNA has partial complementarity in the seed region with unintended genes. Here, we describe the rational designing of functional, off-target effect-reduced siRNAs using siDirect 2.0 Web server (http://siDirect2.RNAi.jp/). By using the default parameters, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in the RefSeq database.

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Acknowledgement

This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan to YN and KU-T.

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Authors and Affiliations

  1. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan

    Yuki Naito & Kumiko Ui-Tei

Authors
  1. Yuki Naito
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  2. Kumiko Ui-Tei
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Corresponding author

Correspondence to Kumiko Ui-Tei .

Editor information

Editors and Affiliations

  1. , Lineberger Comprehensive Cancer Center, University of North Carolina, West Drive 450, Chapel Hill, 27599, North Carolina, USA

    Debra J. Taxman

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Naito, Y., Ui-Tei, K. (2013). Designing Functional siRNA with Reduced Off-Target Effects. In: Taxman, D. (eds) siRNA Design. Methods in Molecular Biology, vol 942. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-119-6_3

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  • DOI: https://doi.org/10.1007/978-1-62703-119-6_3

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-118-9

  • Online ISBN: 978-1-62703-119-6

  • eBook Packages: Springer Protocols

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