Conformationally locked aryl C-nucleosides: synthesis of phosphoramidite monomers and incorporation into single-stranded DNA and LNA (locked nucleic acid)

Abstract

Synthesis of a series of LNA-type β-configured C-aryl nucleosides, i.e., 2′-O,4′-C-methylene-β-D-ribofuranosyl derivatives containing phenyl, 4-fluoro-3-methylphenyl, 1-naphthyl, 1-pyrenyl and 2,4,5-trimethylphenyl groups as aglycons, has been accomplished. The key synthetic step consisted of stereoselective Grignard reactions of the cyclic aldehyde 11 followed by cyclization to give the bicyclic core structure with a locked N-type furanose conformation as confirmed by NOE experiments on the di-O-p-methoxybenzyl derivatives 13a–13e and an X-ray crystallographic study of the phenyl derivative 14a. The phosphoramidite approach was used for automated incorporation of the LNA-type β-configured C-aryl monomers 17a–17e into short DNA and 2′-OMe-RNA/LNA strands. It is shown that universal hybridization can be obtained with a conformationally restricted monomer as demonstrated most convincingly for the pyrene LNA monomer 17d, both in a DNA context and in an RNA-like context. Increased binding affinity of oligonucleotide probes for universal hybridization can be induced by combining the pyrene LNA monomer 17d with affinity-enhancing 2′-OMe-RNA/LNA monomers.