Structure of the A-form and B-form of DNA from deuterium NMR line shape simulation

Alexander A. Nevzorov, Stephan Moltke, Michael F. Brown

Research output: Contribution to journalArticle

15 Scopus citations

Abstract

Simulation of experimental solid-state deuterium (2H) NMR spectra of nucleic acid fibers allows one to deduce important microscopic information about the orientation of the base pairs and the helix axis disorder. However, existing interpretations of the 2H NMR spectra of Na-DNA at low humidity are not in complete agreement with the X-ray results. Here we have successfully explained 2H NMR spectra of oriented films of both Li-DNA and Na-DNA with the purine bases specifically deuterated at position C8. The transformation of the coupling tensor from the principal axis system to the laboratory frame has been expanded into four subtransformations, including the crystallographically defined base plane tilt and roll angles. Alternative treatments in terms of noncollective or collective helix axis disorder are considered, and the appropriate powder-pattern limits are recovered. The 2H NMR spectral line shapes have been calculated by using the Monte Carlo method, i.e., by randomly sampling over the static uniaxial distributions of the base pairs and helix axes. The results of the simulations and the structural parameters are in excellent agreement with X-ray diffraction studies, which indicate the presence of either the A-form or B-form of DNA under the given experimental conditions. Only a static distribution of base pairs is needed to account for the spectral line shapes on the 2H NMR time scale, whereas the effects of faster librational motions are contained in the intrinsic line widths and the effective coupling constants. The present 2H NMR approach can aid in developing a more comprehensive picture of DNA conformation and dynamics as an adjunct to X-ray crystallography, fluorescence depolarization, and light-scattering methods, and moreover may prove useful in studies of protein-nucleic acid interactions.

Original languageEnglish (US)
Pages (from-to)4798-4805
Number of pages8
JournalJournal of the American Chemical Society
Volume120
Issue number19
DOIs
StatePublished - May 20 1998

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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