Skip Navigation



Nucleic Acids Research Advance Access published online on October 8, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp835
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2492K) Freely available
Right arrow Screen PDF (834K) Freely available
Right arrow Supplementary Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Huang, H.
Right arrow Articles by Liang, Z.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Huang, H.
Right arrow Articles by Liang, Z.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs

Huang Huang1, Renping Qiao2, Deyao Zhao3, Tong Zhang2, Youxian Li1, Fan Yi1, Fangfang Lai1, Junmei Hong1, Xianfeng Ding3, Zhenjun Yang2, Lihe Zhang2, Quan Du1,* and Zicai Liang1,*

1Institute of Molecular Medicine, Peking University, Beijing 100871, 2The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing 100083 and 3School of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China

*To whom correspondence should be addressed. Tel:+86 10 62769861; Fax: +86 10 62769862; Email: quan.du{at}pku.edu.cn Correspondence may also be addressed to Zicai Liang. Tel:+86 10 62769862; Fax: +86 10 62769862; Email: liangz{at}edu.pku.cn

Received August 27, 2009. Revised September 18, 2009. Accepted September 18, 2009.

Silencing specificity is a critical issue in the therapeutic applications of siRNA, particularly in the treatment of single nucleotide polymorphism (SNP) diseases where discrimination against single nucleotide variation is demanded. However, no generally applicable guidelines are available for the design of such allele-specific siRNAs. In this paper, the issue was approached by using a reporter-based assay. With a panel of 20 siRNAs and 240 variously mismatched target reporters, we first demonstrated that the mismatches were discriminated in a position-dependent order, which was however independent of their sequence contexts using position 4th, 12th and 17th as examples. A general model was further built for mismatch discrimination at all positions using 230 additional reporter constructs specifically designed to contain mismatches distributed evenly along the target regions of different siRNAs. This model was successfully employed to design allele-specific siRNAs targeting disease-causing mutations of PIK3CA gene at two SNP sites. Furthermore, conformational distortion of siRNA-target duplex was observed to correlate with the compromise of gene silencing. In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.