title: Chemical modification patterns compatible with high potency dicer-substrate small interfering RNAs.
abstract: Dicer-substrate small interfering RNAs (DsiRNAs) are synthetic RNA duplexes that are processed by Dicer into 21-mer species and show improved potency as triggers of RNA interference, particularly when used at low dose. Chemical modification patterns that are compatible with high potency 21-mer small interfering RNAs have been reported by several groups. However, modification patterns have not been studied for Dicer-substrate duplexes. We therefore synthesized a series of chemically modified 27-mer DsiRNAs and correlated modification patterns with functional potency. Some modification patterns profoundly reduced function although other patterns maintained high potency. Effects of sequence context were observed, where the relative potency of modification patterns varied between sites. A modification pattern involving alternating 2'-O-methyl RNA bases was developed that generally retains high potency when tested in different sites in different genes, evades activation of the innate immune system, and improves stability in serum.
authors.affiliation: Integrated DNA Technologies, Inc 1710 Commercial Park, Coralville, IA 52241, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Collingwood
authors.forename: Scott D
authors.initials: SD
authors.lastname: Rose
authors.forename: Lingyan
authors.initials: L
authors.lastname: Huang
authors.forename: Chris
authors.initials: C
authors.lastname: Hillier
authors.forename: Mohammad
authors.initials: M
authors.lastname: Amarzguioui
authors.forename: Merete T
authors.initials: MT
authors.lastname: Wiiger
authors.forename: Harris S
authors.initials: HS
authors.lastname: Soifer
authors.forename: John J
authors.initials: JJ
authors.lastname: Rossi
authors.forename: Mark A
authors.initials: MA
authors.lastname: Behlke
mesh_terms: D001483:Base Sequence; D002478:Cells, Cultured; D053487:DEAD-box RNA Helicases / Q000032:analysis / Q000378:metabolism*; D004722:Endoribonucleases / Q000032:analysis / Q000378:metabolism*; D017930:Genes, Reporter; D005822:Genetic Vectors; D049452:Green Fluorescent Proteins / Q000235:genetics; D045325:HCT116 Cells; D006367:HeLa Cells; D006801:Humans; D016898:Interferon-alpha / Q000032:analysis / Q000378:metabolism; D007700:Kinetics; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D049410:Luciferases, Renilla / Q000378:metabolism; D008969:Molecular Sequence Data; D010957:Plasmids; D012313:RNA / Q000235:genetics; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000235:genetics; D034741:RNA, Small Interfering / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics*; D012015:Reference Standards; D043244:Ribonuclease III; D012680:Sensitivity and Specificity; D013379:Substrate Specificity; D014162:Transfection
chemical_list: D016898:Interferon-alpha; D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins; D012313:RNA; D049410:Luciferases, Renilla; D004722:Endoribonucleases; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases