SpringerProtocols: Abstract: Guidelines for the Selection of Effective Short-Interfering RNA Sequences for Functional Genomics

Guidelines for the Selection of Effective Short-Interfering RNA Sequences for Functional Genomics

By: Kumiko Ui-Tei², Yuki Naito², Kaoru Saigo²

Abstract

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To avoid long-double-stranded-RNA-dependent interferon response, short-interfering RNAs (siRNAs) are widely used for RNA interference (RNAi) in mammalian cells. siRNA-based RNAi, however, may not be readily available for the large-scale gene silencing essential for systematic functional genomics, because only a limited fraction of siRNAs is capable of inducing effective mammalian RNAi. siRNAs correctly designed for the knockdown of a particular gene may also destroy the functions of unrelated genes. Here, we describe algorithms by which these serious setbacks can be eliminated in mammalian functional genomics using RNAi and a Web-based online software system for computing highly functional siRNA sequences with maximal target-specificity in mammalian RNAi.

Affiliation(s): (2) Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo

Book Title: Target Discovery and Validation Reviews and Protocols: Volume 2: Emerging Molecular Targets and Treatment Options

Series: Methods in Molecular Biology | Volume: 361 | Pub. Date: Feb-05-2007 | Page Range: 201-216 | DOI: 10.1385/1-59745-208-4:201

Subject: Pharmacology/Toxicology

Key Words: Mammalian RNAi - functional siRNA - off-target effects - target assay - siDirect

References

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