title: RNA major groove modifications improve siRNA stability and biological activity.
abstract: RNA 5-methyl and 5-propynyl pyrimidine analogs were substituted into short interfering RNAs (siRNAs) to probe major groove steric effects in the active RNA-induced silencing complex (RISC). Synthetic RNA guide strands containing varied combinations of propynyl and methyl substitution revealed that all C-5 substitutions increased the thermal stability of siRNA duplexes containing them. Cellular gene suppression experiments using luciferase targets in HeLa cells showed that the bulky 5-propynyl modification was detrimental to RNA interference activity, despite its stabilization of the helix. Detrimental effects of this substitution were greatest at the 5'-half of the guide strand, suggesting close steric approach of proteins in the RISC complex with that end of the siRNA/mRNA duplex. However, substitutions with the smaller 5-methyl group resulted in gene silencing activities comparable to or better than that of wild-type siRNA. The major groove modifications also increased the serum stability of siRNAs.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Terrazas
authors.forename: Eric T
authors.initials: ET
authors.lastname: Kool
mesh_terms: D006367:HeLa Cells; D006801:Humans; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011741:Pyrimidine Nucleosides / Q000737:chemistry; D034622:RNA Interference; D020871:RNA Stability; D034741:RNA, Small Interfering / Q000097:blood / Q000737:chemistry*; D058727:RNA, Small Untranslated
chemical_list: D011741:Pyrimidine Nucleosides; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated