Synthesis and nucleic-acid-binding properties of sulfamide- and 3′-N-sulfamate-modified DNA

Abstract

A novel synthetic route for the preparation of sulfamide- and 3′-N-sulfamate-modified dinucleosides has been developed. The synthesis utilises 4-nitrophenyl chlorosulfate to prepare 4-nitrophenyl 3′- or 5′-sulfamates (e.g., 18 and 27), which couple smoothly with the alcohol or amine functionalities of other nucleosides. The conformational properties of the sulfamide- and 3′-N-sulfamate-modified dinucleosides d(TnsnT) and d(TnsoT) were compared with the native dinucleotide d(TpT) using NMR and CD spectroscopy. Whilst both modifications result in a shift in the conformational equilibrium of the 5′-terminal ribose rings from C2′-endo to a preferred C3′-endo conformation, only the 3′-N-sulfamate-modified dimer exhibits an increased propensity to adopt a base-stacked helical conformation. Incorporation of the sulfamide- and 3′-N-sulfamate modifications into the DNA sequence d(GCGT₁₀GCG) allowed the duplex melting temperature to be determined using UV thermal denaturation experiments. This reveals that the sulfamide modification significantly destabilises duplexes with both complementary DNA and RNA. However, the 3′-N-sulfamate modification has little effect on duplex stability and even stabilises DNA duplexes at low salt concentration. These results indicate that the 3′-N-sulfamate group is one of the most promising neutral replacements of the phosphodiester group in nucleic acids, that have been developed to date, for therapeutic and other important applications.