Journal of Biosciences

, Volume 8, Issue 3–4, pp 553–562 | Cite as

Quantitative internuclear distancesvia two-dimensional nuclear magnetic resonance spectra: A test case and a DNA octamer duplex

  • Thomas L. James
  • Gregory B. Young
  • Michelle S. Broido
  • Joe W. Keepers
  • Nadege Jamin
  • Gerald Zon


Two-dimensional proton nuclear magnetic resonance nuclear Overhauser effect experiments have been performed at a series of mixing times on proflavine and on a DNA octamer duplex [d-(GGAATTCC)]2 in solution. Using the complete matrix approach recently explored theoretically (Keepers and James, 1984), proton-proton internuclear distances were determined quantitatively for proflavine from the two-dimensional nuclear Overhauser effect results. Since proflavine is a rigid molecule with X-ray crystal structure determined, interproton distances obtained from the two-dimensional nuclear Overhauser effect experiments in solution can be compared with those for the crystalline compound agreement is better than 10 %. Experimental two-dimensional nuclear Overhauser effect spectral data for [d-(GGAATTCC)]2 were analyzed by comparison with theoretical two-dimensional nuclear Overhauser effect spectra at each mixing time calculated using the complete 70 × 70 relaxation matrix. The theoretical spectra were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on similarity of the octamer's six internal residues with those of [d-(CGCGAATTCGCG)]2, for which the crystal structure has been determined. Neither the standard B-DNA nor the energy-minimized structure yield theoretical two-dimensional nuclear Overhauser effect spectra which accurately reproduce all experimental peak intensities. But many aspects of the experimental spectra can be represented by both the B-DNA and the energy-minimized structure. In general, the energy-minimized structure yields theoretical two-dimensional nuclear Overhauser effect spectra which mimic many, if not all, features of the experimental, spectra including structural characteristics at the purine-pyrimidine junction.


Two-dimensional nuclear Overhauser effect nuclear magnetic resonance DNA nucleotides internuclear distances 

Abbreviations used


Two-dimensional nuclear Overhauser effect


relaxation time


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Copyright information

© Printed in India 1985

Authors and Affiliations

  • Thomas L. James
    • 1
  • Gregory B. Young
    • 1
  • Michelle S. Broido
    • 1
    • 2
  • Joe W. Keepers
    • 1
    • 3
  • Nadege Jamin
    • 1
  • Gerald Zon
    • 1
    • 4
  1. 1.Department of Pharmaceutical Chemistry, School of PharmacyUniversity of CaliforniaSan FranciscoUSA
  2. 2.Department of ChemistryHunter College and Graduate Center of the City University of New YorkNew YorkUSA
  3. 3.Department of ChemistryRutgers UniversityNew BrunswickUSA
  4. 4.National Center for Drugs and BiologicsFood and Drug AdministrationBethesdaUSA

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