The structure of the double-stranded RNA pentamer 5'(CACAG) . 5'(CUGUG) determined by nuclear Overhauser enhancement measurements: interproton distance determination and structure refinement on the basis of X-ray coordinates

Eur J Biochem. 1985 Aug 15;151(1):153-65. doi: 10.1111/j.1432-1033.1985.tb09080.x.


The structure in solution of the duplex RNA pentamer 5'(CACAG) . 5'(CUGUG), comprising the stem of the T psi C loop of yeast tRNAPhe, has been investigated by means of one- and two-dimensional nuclear Overhauser enhancement measurements. All non-exchangeable base and sugar proton resonances with the exception of the H5'/H5" sugar resonances are assigned in a sequential manner. From the relative intensities of the cross-peaks obtained in the pure-phase absorption two-dimensional nuclear Overhauser enhancement spectra at several mixing times, it is deduced that the RNA pentamer adopts an A-type conformation in solution. Cross-relaxation rates and interproton distances are determined from the time dependence of the nuclear Overhauser effects, principally by one-dimensional measurements. The structure of the RNA pentamer is then refined by restrained least-squares minimization on the basis of both distance and planarity restraints using fibre diffraction data as an initial model. The refined structure of the RNA pentamer is of the A type but exhibits local structural variations in glycosidic bond and backbone torsion angles as well as in propeller twist, base roll and base tilt angles.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chemical Phenomena
  • Chemistry
  • Chemistry, Physical
  • Glycosides
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Nucleic Acid Conformation
  • Oligonucleotides*
  • Oligoribonucleotides*
  • Protons
  • RNA, Double-Stranded*
  • Solutions


  • Glycosides
  • Oligonucleotides
  • Oligoribonucleotides
  • Protons
  • RNA, Double-Stranded
  • Solutions