Quantitative gamma-HCNCH: determination of the glycosidic torsion angle chi in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy

J Biomol NMR. 2007 Sep;39(1):17-29. doi: 10.1007/s10858-007-9167-5. Epub 2007 Jul 20.

Abstract

A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides. The quantitative Gamma-HCNCH measures the dipolar cross-correlated relaxation rates Gamma(DD,DD)(C8H8,C1'H1') (pyrimidines) and Gamma(DD,DD)(C6H6,C1'H1') (purines). Cross-correlated relaxation rates of a (13)C,(15)N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded chi-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the chi-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / chemistry
  • Base Sequence
  • Glycosides / chemistry*
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / genetics
  • Pyrimidines / chemistry
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • Rotation*
  • Solutions

Substances

  • Glycosides
  • Oligoribonucleotides
  • Pyrimidines
  • RNA, Viral
  • Solutions
  • Adenosine