title: Rational siRNA design for RNA interference.
abstract: Short-interfering RNAs suppress gene expression through a highly regulated enzyme-mediated process called RNA interference (RNAi). RNAi involves multiple RNA-protein interactions characterized by four major steps: assembly of siRNA with the RNA-induced silencing complex (RISC), activation of the RISC, target recognition and target cleavage. These interactions may bias strand selection during siRNA-RISC assembly and activation, and contribute to the overall efficiency of RNAi. To identify siRNA-specific features likely to contribute to efficient processing at each step, we performed a systematic analysis of 180 siRNAs targeting the mRNA of two genes. Eight characteristics associated with siRNA functionality were identified: low G/C content, a bias towards low internal stability at the sense strand 3'-terminus, lack of inverted repeats, and sense strand base preferences (positions 3, 10, 13 and 19). Further analyses revealed that application of an algorithm incorporating all eight criteria significantly improves potent siRNA selection. This highlights the utility of rational design for selecting potent siRNAs and facilitating functional gene knockdown studies.
authors.affiliation: Dharmacon, Inc., 2650 Crescent Drive, Suite 100, Lafayette, Colorado 80026, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: Reynolds
authors.forename: Devin
authors.initials: D
authors.lastname: Leake
authors.forename: Queta
authors.initials: Q
authors.lastname: Boese
authors.forename: Stephen
authors.initials: S
authors.lastname: Scaringe
authors.forename: William S
authors.initials: WS
authors.lastname: Marshall
authors.forename: Anastasia
authors.initials: A
authors.lastname: Khvorova
mesh_terms: D000818:Animals; D001483:Base Sequence; D021983:Cyclophilins / Q000235:genetics / Q000378:metabolism; D004175:Diptera; D005818:Genetic Engineering / Q000379:methods*; D006801:Humans; D008156:Luciferases / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D019696:Peptidylprolyl Isomerase; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000032:analysis / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA
chemical_list: D034741:RNA, Small Interfering; C081786:cyclophilin B; D008156:Luciferases; D021983:Cyclophilins; D019696:Peptidylprolyl Isomerase