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

Nucleic Acids Res. 1996 Jan 15;24(2):354-60. doi: 10.1093/nar/24.2.354.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Circular Dichroism
  • Deoxyribose / chemistry
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • Oligodeoxyribonucleotides / chemistry*
  • RNA / chemistry

Substances

  • Oligodeoxyribonucleotides
  • Deoxyribose
  • RNA