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Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers

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siRNA Design

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

Abstract

Synthetic shRNAs that are too short to be Dicer substrates (short shRNAs or sshRNAs) can be highly potent RNAi effectors when properly designed, with activities similar to or more potent than the more commonly used siRNAs targeting the same sequences. sshRNAs can be designed in two possible orientations: left- or right-hand loop, designated L-sshRNAs and R-sshRNAs, respectively. Because L- and R-sshRNAs are processed by the RNAi machinery in different ways, optimal designs for the two formats diverge in several key aspects. Here, we describe the principles of design and chemical modification of highly effective L- and R-sshRNAs.

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Author information

Authors and Affiliations

  1. SomaGenics, Inc., Santa Cruz, CA, USA

    Anne Dallas & Brian H. Johnston

  2. Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA

    Brian H. Johnston

Authors
  1. Anne Dallas
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  2. Brian H. Johnston
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Corresponding author

Correspondence to Brian H. Johnston .

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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Dallas, A., Johnston, B.H. (2013). Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers. 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_15

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  • DOI: https://doi.org/10.1007/978-1-62703-119-6_15

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-118-9

  • Online ISBN: 978-1-62703-119-6

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