NMR assignments and solution conformation of the DNA.RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC)

Eur J Biochem. 1993 Jul 15;215(2):297-306. doi: 10.1111/j.1432-1033.1993.tb18035.x.

Abstract

Nearly complete assignments of the 1H-NMR spectrum of the DNA.RNA hybrid d(GTGAACTT).r(AAGUUCAC) have been obtained by two-dimensional methods. Three-bond coupling constants measured from cross-sections of two-dimensional NOE spectra and double quantum-filtered correlation spectra showed that the sugars in the DNA strand are predominantly in the S domain of puckers, whereas the ribofuranoses are mainly C3'-endo. Analysis of time-dependent NOE intensities from one- and two-dimensional experiments showed that the glycosidic torsion angles in the DNA strand are near -120 degrees, whereas those in the RNA strand are in the range- 140 degrees to -160 degrees. These nucleotide conformations correspond to those typically found in B-DNA and A-RNA, respectively. The circular dichroism of the duplex is similar to that of A-form RNA, consistent with a global A-like conformation. A large number of duplex structures was generated in which the nucleotides were fixed in the experimentally determined conformations. A subset of these structures was found that satisfied the internucleotide NOE intensities, backbone constraints and had acceptable Lennard-Jones energies. The base pairs in the duplex were found to have positive inclinations, a translation (Dx) of about 0.4 nm from the helix axis, and more than 10 bp/turn on average. This implies a helical structure in the A family of conformations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Circular Dichroism
  • DNA / chemistry*
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization*
  • Oligodeoxyribonucleotides / chemistry*
  • Oligodeoxyribonucleotides / isolation & purification
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / isolation & purification
  • Protons
  • RNA / chemistry*

Substances

  • Oligodeoxyribonucleotides
  • Oligoribonucleotides
  • Protons
  • RNA
  • DNA