A Critique of the Interpretation of Nuclear Overhauser Effects of Duplex DNA

The shape of a duplex DNA molecule can be modeled as a cylinder with symmetry axis z. The effective correlation time of an internuclear vector depends on the orientation of the vector to the symmetry axis as well as the internuclear distance and extent of internal motion. Calculations are presented which illustrate these principles. Since the effective correlation times can depend on the orientation of internuclear vectors so do NMR relaxation parameters such as the rate of buildup of nuclear Overhauser effects and the rates of spin diffusion. The approach is illustrated using a model nucleotide to show how the magnetization transfer can be affected by the orientation and spin diffusion rates.