title: The contributions of dsRNA structure to Dicer specificity and efficiency.
abstract: Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.
authors.affiliation: Dharmacon Inc., 2650 Crescent Dr., Suite #100, Lafayette, CO 80026, USA.
authors.forename: Annaleen
authors.initials: A
authors.lastname: Vermeulen
authors.forename: Linda
authors.initials: L
authors.lastname: Behlen
authors.forename: Angela
authors.initials: A
authors.lastname: Reynolds
authors.forename: Alexey
authors.initials: A
authors.lastname: Wolfson
authors.forename: William S
authors.initials: WS
authors.lastname: Marshall
authors.forename: Jon
authors.initials: J
authors.lastname: Karpilow
authors.forename: Anastasia
authors.initials: A
authors.lastname: Khvorova
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D053487:DEAD-box RNA Helicases; D004722:Endoribonucleases / Q000378:metabolism*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020365:RNA Helicases / Q000378:metabolism*; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D043244:Ribonuclease III; D013379:Substrate Specificity
chemical_list: D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; D004722:Endoribonucleases; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases