Oligonucleotide analogues containing (2″S)- and (2″R)-2′-O,3′-C-((2″-C-hydroxymethyl)ethylene)-linked bicyclic nucleoside monomers:† Synthesis, RNA-selective binding, and diastereoselective formation of a very stable homocomplex based on T∶T base pairing

Abstract

The 2′-O,3′-C-[(2″R)-2″-C-(acetoxymethyl)ethylene]-linked and 2′-O,3′-C-[(2″S)-2″-C-(acetoxymethyl)ethylene]-linked bicyclic thymine nucleosides 12R and 12S have been synthesized and transformed into the phosphoramidite derivatives 14R and 14S, respectively. On an automated DNA-synthesizer the novel 2′-O,3′-C-[(2″-C-hydroxymethyl)ethylene]-linked oligonucleotide analogues (2″R)-2″-hydroxymethyl-2′,3′-BcNA (R) and (2″S)-2″-hydroxymethyl-2′,3′-BcNA (S) have been prepared. The thermal stability of complexes involving these oligonucleotide analogues has been evaluated towards complementary single-stranded DNA and RNA and compared with the thermal stability of reference duplexes involving DNA and 2′-O,3′-C-ethylene-linked 2′,3′-BcNA (B). Oligonucleotide 5′-S₁₃T exhibited RNA-selective binding with moderately enhanced thermal stability relative to the corresponding unmodified control. Remarkably strong intermolecular self-association was observed for 5′-R₁₃T, but not for 5′-S₁₃T.