(2′-5′)-Oligo-3′-Deoxynucleotides: Selective Binding to Single-Stranded RNA but Not DNA

Abstract

Oligodeoxynucleotides with (2′-5′) internucleotide linkages have been synthesized on a solid support via standard cyanoethyl phosphoramidite chemistry. This simple change in the oligonucleotide bond connectivity led to unique properties. UV melting temperature experiments indicate that the (2′-′)-oligo-3′-deoxyadenylates, (2′-5′)-3′-dA₈ and (2′-5′)-3′-dA₈(s) phosphorothioate, hybridize selectively to single-stranded RNA but not DNA. The complex (2′-5′)-3′-dA₈:poly (U) (T_m = 32°C) was nearly as stable as the natural (3′-5′)-2′-dA₈ and poly (U) (T_m = 33°C) in 130 mM NaCl, and 10 mM phosphate buffer (pH 7.5). However, no association was observed upon mixing (2′-5′)-3′-dA₈ and poly (dT). The (2′-5′) linkages also confer greater resistance to exo- and endonucleolytic degradation compared with (3′-5′)-linked oligomers. The rate of degradation of (2′-5′)-3′-dA₈ was almost four times less than that of (3′-5′)-2′-dA₈ in cell culture medium containing 10% heat-inactivated fetal calf serum. An increase in stability for (2′-5′)-3′-dA₈ against endonuclease activity was observed in both cytoplasmic and nuclear extracts. The nucleic acid selectivity of (2′-5′)-oligo-3′-deoxynucleotides may represent an important design feature to improve the efficacy of antisense oligonucleotides.