An oligodeoxyribonucleotide N3'->P5' phosphoramidate duplex forms an A-type helix in solution

The solution conformations of the dinucleotide d(TT) and the modified duplex d(CGCGAATTCGCG)(2) with N3'-->P5' phosphoramidate internucleoside linkages have been studied using circular dichroism (CD) and NMR spectroscopy. The CD spectra indicate that the duplex conformation is similar to that of isosequential phosphodiester RNA, an A-type helix, and is different from that of DNA, a B-type helix. NMR studies of model dimers d(TpT) and N3'-->P5' phosphoramidate d(TnpT) show that the sugar ring conformation changes from predominantly C2'-endo to C3'-endo when the 3'-phosphoester is replaced by a phosphoramidate group, Two-dimensional NMR (NOESY, DQF-COSY and TOCSY spectral studies of the duplex provide additional details about the A-type duplex conformation of the oligonucleotide phosphoramidate and confirm that all furanose rings of 3'-aminonucleotides adopt predominantly N-type sugar puckering.