Analogues of a Locked Nucleic Acid with Three-Carbon 2‘,4‘-Linkages:  Synthesis by Ring-Closing Metathesis and Influence on Nucleic Acid Duplex Stability and Structure

Two bicyclic 2‘-deoxynucleoside analogues containing a saturated and an unsaturated three-carbon 2‘,4‘-linkage, respectively, have been synthesized using a ring-closing metathesis-based linear strategy starting from uridine. Both analogues have been incorporated into oligodeoxynucleotide sequences and increased the stability of DNA:RNA hybrid duplexes (ΔT_m ∼ 2.5−5.0 °C per modification) and decreased the stability of dsDNA duplexes (ΔT_m ∼ 2.5−1.0 °C per modification). CD spectroscopy revealed that the bicyclic nucleosides induced formation of A-type-like duplexes albeit to a lesser degree than found for locked nucleic acid (LNA) monomers. From the CD data and UV melting analysis, we propose that the 2‘-oxygen atom of the bicyclic moiety is essential for the formation of stabilized A-type-like dsDNA but not for the formation of a stabilized A-type DNA:RNA hybrid.