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Nucleic Acids Research, Vol 24, Issue 2 354-360, Copyright © 1996 by Oxford University Press

ARTICLES

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

D Ding, SM Grayaznov, DH Lloyd, S Chandrasekaran, S Yao, L Ratmeyer, Y Pan and WD Wilson
Department of Chemistry, Georgia State University, Atlanta, 30303, USA.

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, a 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 spectra) 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.
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