Synthesis of oligodeoxyribonucleotide N3′→P5′ phosphoramidates

Open Access
Publisher Website
Google Scholar
Abstract
An efficient synthesis of the novel nucleic acid analogs oligodeoxyribonucleotide N3′→P5′ phosphoramidates, where the 3′-oxygen is substituted by a 3′-nitrogen, is described. Synthesis of the title compounds was accomplished by the following synthetic steps. First, 5–O-DMT base-protected-3′-amino-2′,3′-dkieoxynucleosides were prepared. The 3′-aminopyrimldlnes were obtained via the corresponding 2′,3′-anhydronucleosides, whereas 3′-amlnopurines were derived via 2′-deoxyxylo precursors. Second, using the prepared 3′-aminonucleosides, oligonucleotide N3′→P5′ phosphoramidates were synthesized on a solid support. Oligonucleotide chain assembly was based upon a carbon tetrachloride-driven oxidatlve coupling of the appropriately protected 3′-amlnonucleosides with the 5′-H-phosphonate diester group, resulting in the formation of an intemucleoside phosphoramldate link. Fully deprotected oligonucleotide N3′→P5′ phosphoramidates were characterized by ion exchange and reversed phase HPLC, capillary and slab gel etectrophoresis and by 31P NMR analysis. Oligonucleotide N3′→P5′ phosphoramidates form remarkably stable duplexes with complementary RNA strands and also with themselves, where the melting temperature of the complexes exceeded that for the parent phosphodiester compounds by 26–33°C. Additionally, duplexes formed by oligonucleo ide phosphoramidates with singlestranded DNA were also more thermally stable than those formed by phosphodiesters. The described properties indicate that these compounds may have great potential in oligonucleotide-based diagnostics and therapeutic applications.