TIME-DEPENDENCE OF NUCLEAR OVERHAUSER EFFECTS OF DUPLEX DNA FROM MOLECULAR-DYNAMICS TRAJECTORIES

The buildup rates of nuclear Overhauser effects (NOEs) for all of thc protons of a DNA dodecamer have been calculated on the basis of molecular dynamics trajectories of the duplex. The buildup rates were determined by taking into consideration the orientation of the proton-proton vectors to the symmetry axis, the extent of internal motion of the vectors and the interactions between all pairs of protons and the overall anisotropic tumbling of the duplex. The time dependence of the NOEs was determined by solving the generalized Bloch equation by numerical integration for all protons with full relaxation methods. These calculations show that the initial rates of NOE buildups are not always related to the inverse sixth power of the interproton distance. Results also indicate that different simulation models predict distinguishably different experimental data and that, within a particular simulation, distinguishably different experimental data are predicted for distinct residues in the DNA duplex. With these methods, experimental data can be used to discriminate between proposed structural and dynamical models of DNA obtained from molecular dynamics simulations.