Synthesis and Properties of Oligonucleotides Containing 2′‐O,4′‐C‐Ethylene‐Bridged 5‐Methyluridine with Exocyclic Methylene and Methyl Groups in the Bridge

Abstract

Novel 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) analogs with exocyclic methylene and (R)-methyl groups at the 6'position were synthesized. The obtained 6'-methylene-ENA and 6'R-Me-ENA were incorporated into oligonucleotides, and their properties were compared with those of the corresponding natural, ENA-, and 6'S-Me-ENA-modified oligonucleotides. The duplex-stabilizing ability of 6'-methylene-ENA and 6'R-Me-ENA with single-stranded RNA (ssRNA) was similar to that of ENA and 6'S-Me-ENA under both dilute and molecular crowding conditions. On the other hand, oligonucleotides containing 6'-methylene-ENA and 6'R-Me-ENA formed stable triplexes with double-stranded DNA (dsDNA) in comparison with those containing 6'S-Me-ENA. Their thermodynamic properties were also calculated to explore the influence of the substituents introduced at the 6'-position of ENA. Moreover, oligonucleotides with ENA analogs exhibited excellent resistance against nucleases. These results suggest that 6'-methylene-ENA and 6'R-Me-ENA are promising candidates for targeting ssRNA and dsDNA.