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, 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.
Ding
D
D
Department of Chemistry, Georgia State University, Atlanta, 30303, USA.
Grayaznov
S M
SM
Lloyd
D H
DH
Chandrasekaran
S
S
Yao
S
S
Ratmeyer
L
L
Pan
Y
Y
Wilson
W D
WD
D001483:Base Sequence; D002942:Circular Dichroism; D003855:Deoxyribose / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D003855:Deoxyribose; D012313:RNA