title: Is irrelevant cleavage the price of antisense efficacy?
abstract: Antisense oligonucleotides are useful reagents for the suppression of gene expression. Their mechanism of action in eukaryotic cells appears to depend heavily on the activity of RNase H, a ubiquitous enzyme that cleaves the mRNA strand of an RNA-DNA duplex. However, the stringency requirements of RNase H are very low, and as little as a 5-base complementary region of oligomer to target may be sufficient to elicit RNase H activity. This would result in scission of nontargeted mRNAs, or what is known as "irrelevant cleavage." One strategy to reduce RNase H competency that has been employed is modification of the oligonucleotide backbone, replacing phosphodiester linkages with uncharged methylphosphonates, which are not RNase H competent. Another strategy involves replacement of deoxyribonucleic acid with 2'-O-alkylribonucleic acid. A third strategy, eliminating RNase H dependency entirely, requires activation of RNase P. The relative merits of these strategies will be discussed in the context of selective inhibition of gene function.
authors.affiliation: Department of Medicine, Columbia University, College of Physicians and Surgeons, 630 W. 168 Street, New York, NY, USA. stein@cuccfa.ccc.columbia.edu
authors.forename: C A
authors.initials: CA
authors.lastname: Stein
mesh_terms: D004247:DNA / Q000378:metabolism; D004722:Endoribonucleases / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D016376:Oligonucleotides, Antisense / Q000737:chemistry / Q000235:genetics / Q000494:pharmacology*; D009943:Organophosphorus Compounds / Q000737:chemistry; D012313:RNA / Q000378:metabolism; D016337:RNA, Catalytic / Q000378:metabolism; D016914:Ribonuclease H / Q000378:metabolism*; D043262:Ribonuclease P
chemical_list: D016376:Oligonucleotides, Antisense; D009943:Organophosphorus Compounds; D016337:RNA, Catalytic; C032627:methylphosphonic acid; D012313:RNA; D004247:DNA; D004722:Endoribonucleases; D016914:Ribonuclease H; C468368:RPP14 protein, human; D043262:Ribonuclease P