Practical treatment of nuclear magnetic resonance relaxation in carbon-13/nitrogen-15-labeled nucleic acids: Application to d(CGCGAATTCGCG).

摘要

A computational approach to the modeling of heteronuclear NMR data is outlined in the relaxation matrix formalism convenient for application to macromolecules. Given a model structure, the principal axis system of the diffusion tensor is computed or taken as that of the moment of inertia tensor. All pair-wise heteronuclear and homonuclear dipolar interaction tensors are then computed in this frame, and the chemical shift anisotropy (CSA) tensors are placed on each nucleus of interest. The latter may be taken from experimental data, or provided by electronic structure calculation at the desired level of theory. Using these data as input, the relaxation rates, R ₁ and R₂, and the ssNOE enhancement are systematically computed. The computed rates are compared to experimental data for the determination of rotational hydrodynamics and/or intramolecular dynamics parameters. No assumptions are made as to the relative orientations of any of the interaction tensors, and fully anisotropic rigid body diffusion is accommodated. The method is useful for testing the validity of a wide range of assumptions often made in the analysis of NMR relaxation data for macromolecular systems. The software package, Y&barbelow;et A&barbelow;nother R&barbelow;elaxation M&barbelow;atrix (YARM) program, was enhanced to perform these calculations. As a model system, a nucleic acid helix, d(CGCGAATTCGCG), D12, was chosen, for which several models exist in the literature. The dynamics of DNA are complex, and the rotational hydrodynamics are deemed indeterminate for data collected at a single field; however, the fast motion parameters of the “model-free” formalism are determined and discussed with respect to the “worm-like” chain model of DNA.