title: The impact of target site accessibility on the design of effective siRNAs.
abstract: Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.
authors.affiliation: Institute of Theoretical Biochemistry (TBI), University of Vienna, Austria.
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.forename: Stefan L
authors.initials: SL
authors.lastname: Ameres
authors.forename: Gregor
authors.initials: G
authors.lastname: Obernosterer
authors.forename: Christoph A
authors.initials: CA
authors.lastname: Gebeshuber
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
authors.forename: Javier
authors.initials: J
authors.lastname: Martinez
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D018390:Gene Targeting / Q000379:methods*; D008956:Models, Chemical; D008957:Models, Genetic; D008969:Molecular Sequence Data; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D034741:RNA, Small Interfering