Naito, Y. et al. dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Res. 33, W589-W591

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: 9.11). 08/2005; 33(Web Server issue):W589-91. DOI: 10.1093/nar/gki419
Source: PubMed


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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    • "To ensure dsRNA specificity and to exclude potential non-specific targets, we used the E-RNAi [43], dsCheck [44] and DEQOR [45] programs to determine the dsRNA sequence. However, because the A. fluviatilis gene sequences are not available, we performed the analyses based on equivalent regions of the GSK-3 orthologous genes and genome sequences of other species (A. "
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    • "However, to reinforce this inactivation, we introduced either another UAS- zfh-2RNAi insertion or the UAS-Dicer-2 (Dcr-2) construct (Dietzl et al., 2007) into some of our mutant combinations. The two RNA interference constructs are directed against different regions of the zfh-2 RNA (data not shown) and the RNAi construct previously described (Terriente et al., 2008) was checked with the DsCheck software (Naito et al., 2005; for possible offtargets (with 0 mismatches) and found to have none. "
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    • "This compares the target sequences with genome sequences of Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Oryza sativa and Rattus Norvegicus from the database and identifies dissimilar regions ( (Naito et al., 2005). Further, the sequence of the selected region was analysed for minimizing the possible homology with other gene sequences of H. armigera using NCBI-BLAST. "
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