Synthesis, nucleic acid hybridization properties and molecular modelling studies of conformationally restricted 3'-O,4' -C-methylene-linked a-L-ribonucleotides

Nucleotides with conformationally restricted carbohydrate rings such as locked nucleic acid (LNA), α-L-LNA or 2′,5′-linked 3′-O,4′-C-methyleribonucleotides exhibit significant potential as building blocks for antigene and antisense strategies. 2′,5′-Linked α-l-ribo configured monomer X (termed α-L-ONA) was designed as a potential structural mimic of α-L-LNA. The corresponding phosphoramidite building block of monomer X was obtained in five steps (10% overall yield) from the easily obtainable thymine derivative 1. Incorporation of monomer X into oligodeoxyribonucleotides (ONs) results in dramatically decreased thermal stabilities with DNA/RNA complements (ΔTm/mod = −11.5 to −17.0 °C) compared to unmodified reference ONs. Less pronounced decreases (ΔTm/mod = −4.5 to −8.5 °C) are observed when monomer X is incorporated into triplex forming ONs and targeted against double-stranded DNA (parallel orientation, pyrimidine motif). This biophysical data, together with modelling studies, suggest that 2′,5′-linked α-L-ONA is a poor structural mimic of α-L-LNA.