Open AccessAn oligodeoxyribonucleotide N3'--> P5' phosphoramidate duplex forms an A-type helix in solution
Author(s) -
Daoyuan Ding,
Sergei Gryaznov,
D. H. Lloyd,
С. Чандрасекаран,
Shijie Yao,
Lynda Ratmeyer,
Yinquan Pan,
W. David Wilson
Publication year - 1996
Publication title -
nucleic acids research
Language(s) - Uncategorized
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/24.2.354
Subject(s) - phosphoramidate , phosphodiester bond , duplex (building) , furanose , oligonucleotide , circular dichroism , biology , helix (gastropod) , crystallography , stereochemistry , nuclear magnetic resonance spectroscopy , two dimensional nuclear magnetic resonance spectroscopy , polynucleotide , dna , rna , biochemistry , chemistry , ring (chemistry) , organic chemistry , ecology , snail , gene
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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