title: Potent RNAi by short RNA triggers.
abstract: RNA interference (RNAi) is a gene-silencing mechanism by which a ribonucleoprotein complex, the RNA-induced silencing complex (RISC) and a double-stranded (ds) short-interfering RNA (siRNA), targets a complementary mRNA for site-specific cleavage and subsequent degradation. While longer dsRNA are endogenously processed into 21- to 24-nucleotide (nt) siRNAs or miRNAs to induce gene silencing, RNAi studies in human cells typically use synthetic 19- to 20-nt siRNA duplexes with 2-nt overhangs at the 3'-end of both strands. Here, we report that systematic synthesis and analysis of siRNAs with deletions at the passenger and/or guide strand revealed a short RNAi trigger, 16-nt siRNA, which induces potent RNAi in human cells. Our results indicate that the minimal requirement for dsRNA to trigger RNAi is an approximately 42 A A-form helix with approximately 1.5 helical turns. The 16-nt siRNA more effectively knocked down mRNA and protein levels than 19-nt siRNA when targeting the endogenous CDK9 gene, suggesting that 16-nt siRNA is a more potent RNAi trigger. In vitro kinetic analysis of RNA-induced silencing complex (RISC) programmed in HeLa cells indicates that 16-nt siRNA has a higher RISC-loading capacity than 19-nt siRNA. These results suggest that RISC assembly and activation during RNAi does not necessarily require a 19-nt duplex siRNA and that 16-nt duplexes can be designed as more potent triggers to induce RNAi.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Chia-Ying
authors.initials: CY
authors.lastname: Chu
authors.forename: Tariq M
authors.initials: TM
authors.lastname: Rana
mesh_terms: D001483:Base Sequence; D006367:HeLa Cells; D006801:Humans; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D034743:RNA-Induced Silencing Complex / Q000737:chemistry / Q000235:genetics*
chemical_list: D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex