Quantitative internuclear distancesvia two-dimensional nuclear magnetic resonance spectra: A test case and a DNA octamer duplex |
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Authors: | Thomas L James Gregory B Young Michelle S Broido Joe W Keepers Nadege Jamin Gerald Zon |
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Institution: | (1) Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, 94143 San Francisco, California, USA;(2) Department of Chemistry, Hunter College and Graduate Center of the City University of New York, 10021 New York, New York, USA;(3) Department of Chemistry, Rutgers University, 08903 New Brunswick, New Jersey, USA;(4) National Center for Drugs and Biologics, Food and Drug Administration, 20205 Bethesda, Maryland, USA |
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Abstract: | 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. |
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Keywords: | Two-dimensional nuclear Overhauser effect nuclear magnetic resonance DNA nucleotides internuclear distances |
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