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Nucleic Acids Research Advance Access originally published online on November 29, 2008
Nucleic Acids Research 2009 37(1):e8; doi:10.1093/nar/gkn953
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Nucleic Acids Research, 2009, Vol. 37, No. 1 e8
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Forward and robust selection of the most potent and noncellular toxic siRNAs from RNAi libraries

Zhen Li1, Yves Fortin2 and Shi-Hsiang Shen1,2,*

1Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4 and 2Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2

*To whom correspondence should be addressed. Tel: +1 514 496 6319; Fax: +1 514 496 6319; Email: shi.shen{at}nrc.ca

Received July 3, 2008. Revised September 29, 2008. Accepted November 11, 2008.

Use of highly potent small interfering RNAs (siRNAs) can substantially reduce dose-dependent cytotoxic and off-target effects. We developed a genetic forward approach by fusing the cytosine deaminase gene with targets for the robust identification of highly potent siRNAs from RNA interference (RNAi) libraries that were directly delivered into cells via bacterial invasion. We demonstrated that two simple drug selection cycles performed conveniently in a single container predominately enriched two siRNAs targeting the MVP gene (siMVP) and one siRNA targeting the egfp gene (siEGFP) in surviving cells and these proved to be the most effective siRNAs reported. Furthermore, the potent siRNAs isolated from the surviving cells possessed noncellular toxic characteristics. Interestingly, the length of highly potent siMVPs identified could be as short as 16-mer, and increasing the length of their native sequences dramatically reduced RNAi potency. These results suggest that the current approach can robustly discover the most potent and nontoxic siRNAs in the surviving cells, and thus has great potential in facilitating RNAi applications by minimizing the dose-dependent and sequence nonspecific side effects of siRNAs.


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