title: Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo.
abstract: RNA interference (RNAi) has become an invaluable tool for functional genomics. A critical use of this tool depends on an understanding of the factors that determine the specificity and activity of the active agent, small interfering RNA (siRNA). Several studies have concluded that tolerance of mutations can be considerable and hence lead to off-target effects. In this study, we have investigated in vivo the toleration of wobble (G:U) mutations in high activity siRNAs against Flap Endonuclease 1 (Fen1) and Aquaporin-4 (Aqp4). Mutations in the central part of the antisense strand caused a pronounced decrease in activity, while mutations in the 5' and 3'ends were tolerated very well. Furthermore, based on analysis of nine different mutated siRNAs with widely differing intrinsic activities, we conclude that siRNA activity can be significantly enhanced by wobble mutations (relative to mRNA), in the 5' terminal of the antisense strand. These findings should facilitate design of active siRNAs where the target mRNA offers limited choice of siRNA positions.
authors.affiliation: Centre for Molecular Biology and Neuroscience (CMBN), and Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo Oslo, Norway. torgeir.holen@medisin.uio.no
authors.forename: Torgeir
authors.initials: T
authors.lastname: Holen
authors.forename: Svein Erik
authors.initials: SE
authors.lastname: Moe
authors.forename: Jan Gunnar
authors.initials: JG
authors.lastname: Sørbø
authors.forename: Trine J
authors.initials: TJ
authors.lastname: Meza
authors.forename: Ole Petter
authors.initials: OP
authors.lastname: Ottersen
authors.forename: Arne
authors.initials: A
authors.lastname: Klungland
mesh_terms: D051401:Aquaporin 4; D020346:Aquaporins / Q000096:biosynthesis / Q000235:genetics; D020029:Base Pairing; D015153:Blotting, Western; D045585:Flap Endonucleases / Q000096:biosynthesis / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D009154:Mutation; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: C496030:AQP4 protein, human; D051401:Aquaporin 4; D020346:Aquaporins; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D045585:Flap Endonucleases; C468317:FEN1 protein, human