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What Parameters to Consider and Which Software Tools to Use for Target Selection and Molecular Design of Small Interfering RNAs

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siRNA Design

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

Abstract

The design of small gene silencing RNAs with a high probability of being efficient still has some elements of an art, especially when the lowest concentration of small molecules needs to be utilized. The design of highly target-specific small interfering RNAs or short hairpin RNAs is even a greater challenging task. Some logical schemes and software tools that can be used for simplifying both tasks are presented here. In addition, sequence motifs and sequence composition biases of small interfering RNAs that have to be avoided because of specificity concerns are also detailed.

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Acknowledgement

The author is very grateful to John Atkins for careful reading of this manuscript and very constructive comments. The work was supported in part by Fred Hutchinson Cancer Center grant DK056465 to animal core facility and by Russian Ministry of Science and Education grant 11.G34.31.0034 to Novosibirsk State University.

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Authors and Affiliations

  1. Department of Human Genetics, University of Utah, Salt Lake City, UT, USA

    Olga Matveeva

  2. Novosibirsk State University, Novosibirsk, Russia

    Olga Matveeva

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  1. Olga Matveeva
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Correspondence to Olga Matveeva .

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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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Matveeva, O. (2013). What Parameters to Consider and Which Software Tools to Use for Target Selection and Molecular Design of Small Interfering RNAs. 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_1

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  • DOI: https://doi.org/10.1007/978-1-62703-119-6_1

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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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