title: Competition for RISC binding predicts in vitro potency of siRNA.
abstract: Short interfering RNAs (siRNA) guide degradation of target RNA by the RNA-induced silencing complex (RISC). The use of siRNA in animals is limited partially due to the short half-life of siRNAs in tissues. Chemically modified siRNAs are necessary that maintain mRNA degradation activity, but are more stable to nucleases. In this study, we utilized alternating 2'-O-methyl and 2'-deoxy-2'-fluoro (OMe/F) chemically modified siRNA targeting PTEN and Eg5. OMe/F-modified siRNA consistently reduced mRNA and protein levels with equal or greater potency and efficacy than unmodified siRNA. We showed that modified siRNAs use the RISC mechanism and lead to cleavage of target mRNA at the same position as unmodified siRNA. We further demonstrated that siRNAs can compete with each other, where highly potent siRNAs can compete with less potent siRNAs, thus limiting the ability of siRNAs with lower potency to mediate mRNA degradation. In contrast, a siRNA with low potency cannot compete with a highly efficient siRNA. We established a correlation between siRNA potency and ability to compete with other siRNAs. Thus, siRNAs that are more potent inhibitors for mRNA destruction have the potential to out-compete less potent siRNAs indicating that the amount of a cellular component, perhaps RISC, limits siRNA activity.
authors.affiliation: ISIS Pharmaceuticals, Carlsbad Research Center, 1896 Rutherford Road, Carlsbad, CA 92008, USA. ekoller@isisph.com
authors.forename: Erich
authors.initials: E
authors.lastname: Koller
authors.forename: Stephanie
authors.initials: S
authors.lastname: Propp
authors.forename: Heather
authors.initials: H
authors.lastname: Murray
authors.forename: Walter
authors.initials: W
authors.lastname: Lima
authors.forename: Balkrishen
authors.initials: B
authors.lastname: Bhat
authors.forename: Thaza P
authors.initials: TP
authors.lastname: Prakash
authors.forename: Charles R
authors.initials: CR
authors.lastname: Allerson
authors.forename: Eric E
authors.initials: EE
authors.lastname: Swayze
authors.forename: Eric G
authors.initials: EG
authors.lastname: Marcusson
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Dean
mesh_terms: D001667:Binding, Competitive; D045744:Cell Line, Tumor; D006801:Humans; D016547:Kinesins / Q000235:genetics; D051059:PTEN Phosphohydrolase / Q000235:genetics; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry*; D034743:RNA-Induced Silencing Complex / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism
chemical_list: C470243:KIF11 protein, human; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex; D012260:Ribonucleases; D051059:PTEN Phosphohydrolase; D016547:Kinesins