dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Nucleic Acids Research (Impact Factor: 8.81). 08/2005; 33(Web Server issue):W589-91. DOI: 10.1093/nar/gki419
Source: PubMed

ABSTRACT Off-target effects are one of the most serious problems in RNA interference (RNAi). Here, we present dsCheck (, web-based online software for estimating off-target effects caused by the long double-stranded RNA (dsRNA) used in RNAi studies. In the biochemical process of RNAi, the long dsRNA is cleaved by Dicer into short-interfering RNA (siRNA) cocktails. The software simulates this process and investigates individual 19 nt substrings of the long dsRNA. Subsequently, the software promptly enumerates a list of potential off-target gene candidates based on the order of off-target effects using its novel algorithm, which significantly improves both the efficiency and the sensitivity of the homology search. The website not only provides a rigorous off-target search to verify previously designed dsRNA sequences but also presents 'off-target minimized' dsRNA design, which is essential for reliable experiments in RNAi-based functional genomics.

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