DNA and RNA analogues – oligonucleotide phosphoramidates with bridging nitrogen

Abstract

Oligonucleotide analogues containing nitrogen replacing either 3′- or 5′-oxygen atoms have been attracting attention of the scientific community for a long time. Originally, it was suggested that these compounds might be used as a functional mimetic of DNA molecules, which could be easier to prepare, due to a higher nucleophilicity of amino vis-a-vie hydroxyl group. Recent advances in development of oligonucleotide-based therapeutic and diagnostic agents significantly increased interest in these compounds as potential antisense and antigene compounds. Among numerous synthesised molecules the N3′→P5′ phosphoramidate oligonucleotides attract particular attention. Uniformly modified oligonucleotide N3′→P5′ phosphoramidates, containing 3′-amino replacing 3′-hydroxyl nucleosides, form very stable duplexes with complementary native phosphodiester DNA, and particularly with RNA strands. The phosphoramidate compounds form extremely stable triple-stranded complexes with single or double-stranded DNA targets and 2′-deoxyoligonucleotide N3′→P5′ phosphoramidates and their duplexes are structurally and functionally similar to those formed by native RNA molecules. This property allowed for application of these compounds as RNA decoys. Further duplex stabilisation was observed for 2′-deoxyoligonucleotide N3′→P5′ oligonucleotides. N3′→P5′ phosphoramidates oligonucleotides are highly resistant to enzymatic digestion by cellular nucleases and their duplexes with complementary RNA strands that are not substrates for RNase H-catalysed hydrolysis in vitro. However, they still exert sequence specific activity in various cellular systems and in vivo in mice, comparable or superior to RNase H-inducing phosphorothioate oligonucleotides. Fluorescently labelled phosphoramidates have also been used as FISH probes for telomeric DNA-directed diagnostic applications.