Hydration effects on the duplex stability of phosphoramidate DNA-RNA oligomers

Abstract

Recent studies on uniformly modified oligonucleotides containing 3'-NHP(O)(O-)O-5' internucleoside linkages (3' amidate) and alternatively modified oligonucleotides containing 3'-O(O-)(O)PNH-5' internucleoside linkages (5' amidate) have shown that 3' amidate duplexes, formed with DNA or RNA complementary strands, are more stable in water than those of the corresponding phosphodiesters. In contrast, 5' amidates do not form duplexes at all. There is no steric reason that the 5' amidate duplex should not form. We demonstrate that these differences arise from differential solvation of the sugar-phosphate backbones. By molecular dynamics calculations on models of l0mer single-stranded DNA and double-stranded DNA-RNA molecules, both with and without the phosphoramidate backbone modifications, we show that the single-stranded 3' amidate and 5' amidate backbones are equally well solvated, but the 5' amidate backbone is not adequately solvated in an A-form duplex. These results are supported by quantum chemical free energy of solvation calculations which show that the 3' amidate backbone is favored relative to the 5' amidate backbone.