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Asymmetrically designed siRNAs and shRNAs enhance the strand specificity and efficacy in RNAi

Research Article

J RNAi Gene Silenc (May 2008), 4(1), 269-280

doi: jrgsxx

Published online: 15 August 2007

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Asymmetrically designed siRNAs and shRNAs enhance the strand specificity and efficacy in RNAi

Hongliu Ding †‡*, Guoqing Liao †¶, Hongyan Wang † and Yejin Zhou ¥

† Department of Biochemistry and Molecular Pharmacology, ‡ Meyers Primary Care Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester , MA 01655, USA

¥ Hefei First Hospital, Anhui Medical University, 390 Huaihe Road, Hefei 230061, China

¶ Current Address: Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha 410008, China

*Correspondence to: Hongliu Ding, Email: hongliu.ding@umassmed.edu, Tel: +508 856 2611, Fax: +8508 856 5024

Received: 30 May 2007, Revised: 14 July 2007, Accepted: 20 July 2007

© Copyright The Authors

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ABSTRACT

RNAi can mediate allele-specific silencing, and offers an attractive approach for treatment of human diseases caused by dominant, gain-of-function gene mutations. However, allele-specific silencing requires that the RNAi target the mutated region of the mRNA, limiting the choices of the target sequences. This often results in the use of a suboptimal siRNAs or shRNAs. Unfavorable strand asymmetry, which leads to the sense strand, rather than the antisense strand, to be incorporated into RNA-induced silencing complex (RISC), can cause poor RNAi efficacy. We systematically tested an approach that places mismatches at or near the 5’ of the antisense strand to create favorable strand asymmetry. Here we show that this approach can enhance the RNAi efficacy of not only siRNAs but also shRNAs synthesized from genes, which can be placed in various viral vectors. Thus, this design of asymmetric shRNAs could be potentially used in silencing dominant, gain-of-function gene mutations for gene therapy.

KEYWORDS: Gene silencing, RNAi therapy, reverse genetics, ALS, neurodegenerative disease, SOD1

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