Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two‐dimensional nuclear Overhauser enhancement spectroscopy

Abstract

Proton 2-dimensional nuclear Overhauser enhancement (2D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)]2 in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 .times. 70 relaxation matrix including all proton dipole interactions and spin diffusion. The theoretical spectra at each mixing time were calculated using 2 structures: a standard B-form DNA structure and an energy-minimized structure based on the similarity of the 6 internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)]2, for which the crystal structure was determined. Neither the standard B-form nor the energy-minimized structure will yield theoretical 2D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. Many features of the experimental spectra can be represented by both the B-form and the energy-minimized structure. Sequence-dependent structural characteristics are manifest in the 2D NOE spectra in particular at the purine-pyrimidine junction as noted previously in the crystal structure. The energy-minimized structure appears to yield theoretical 2D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2D NOE data were consistent with correction times as implied by proton spin-lattice relaxation time measurements; however, better fits of some of the 2D NOE data using small variation in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.