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

Yuki Naito | Zendy; Toshimichi Yamada | Zendy; Teruhiko Matsumiya | Zendy; Kumiko UiTei | Zendy; K. Saigo | Zendy; Shinichi Morishita | Zendy

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

Author(s) -

Yuki Naito,

Toshimichi Yamada,

Teruhiko Matsumiya,

Kumiko UiTei,

K. Saigo,

Shinichi Morishita

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki419

Subject(s) - rna interference , rna silencing , biology , dicer , rna , computational biology , rna editing , small interfering rna , trans acting sirna , genetics , ribonuclease iii , gene

Off-target effects are one of the most serious problems in RNA interference (RNAi). Here, we present dsCheck (http://dsCheck.RNAi.jp/), 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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