title: An assessment of the antisense properties of RNase H-competent and steric-blocking oligomers.
abstract: The antisense activity and gene specificity of two classes of oligonucleotides (ONs) were directly compared in a highly controlled assay. One class of ONs has been proposed to act by targeting the degradation of specific RNAs through an RNase H-mediated mechanism and consists of C-5 propynyl pyrimidine phosphorothioate ONs (propyne-S-ON). The second class of antisense agents has been proposed to function by sterically blocking target RNA formation, transport or translation and includes sugar modified (2'-O-allyl) ONs and peptide nucleic acids (PNAs). Using a CV-1 cell based microinjection assay, we targeted antisense agents representing both classes to various cloned sequences localized within the SV40 large T antigen RNA. We determined the propyne-S-ON was the most potent and gene-specific agent of the two classes which likely reflected its ability to allow RNase H cleavage of its target. The PNA oligomer inhibited T Ag expression via an antisense mechanism, but was less effective than the propyne-S-ON; the lack of potency may have been due in part to the PNAs slow kinetics of RNA association. Interestingly, unlike the 2'-O-allyl ON, the antisense activity of the PNA was not restricted to the 5' untranslated region of the T Ag RNA. Based on these findings we conclude that PNAs could be effective antisense agents with additional chemical modification that will lead to more rapid association with their RNA target.
authors.affiliation: Department of Molecular Cell Biology, Glaxo Research Institute, Research Triangle Park, NC 27709, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Bonham
authors.forename: S
authors.initials: S
authors.lastname: Brown
authors.forename: A L
authors.initials: AL
authors.lastname: Boyd
authors.forename: P H
authors.initials: PH
authors.lastname: Brown
authors.forename: D A
authors.initials: DA
authors.lastname: Bruckenstein
authors.forename: J C
authors.initials: JC
authors.lastname: Hanvey
authors.forename: S A
authors.initials: SA
authors.lastname: Thomson
authors.forename: A
authors.initials: A
authors.lastname: Pipe
authors.forename: F
authors.initials: F
authors.lastname: Hassman
authors.forename: J E
authors.initials: JE
authors.lastname: Bisi
mesh_terms: D000495:Allosteric Site; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D004247:DNA / Q000235:genetics / Q000378:metabolism; D066298:In Vitro Techniques; D007700:Kinetics; D008969:Molecular Sequence Data; D016376:Oligonucleotides, Antisense / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D016914:Ribonuclease H / Q000378:metabolism*
chemical_list: D016376:Oligonucleotides, Antisense; D012313:RNA; D004247:DNA; D016914:Ribonuclease H