STRUCTURE OF THE A-FORM AND B-FORM OF DNA FROM DEUTERIUM NMR LINE-SHAPE SIMULATION

Simulation of experimental solid-stale deuterium (H-2) NMR spectra of nucleic acid fibers allows one to deduce important microscopic informa tion about the orientation of the base pairs and the helix axis disord er. However, existing interpretations of the H-2 NMR spectra of Na-DNA at low humidity are not in complete agreement with the X-ray results. Here we ha iie successfully explained H-2 NMR spectra of oriented fil ms of both Li-DNA and Na-DNA with the purine bases specifically deuter ated at position C8. The transformation of the coupling tensor from th e principal axis system to the laboratory frame has been expanded into four subtransformations, including the crystallographically defined b ase plane tilt and roll angles. Alternative treatments in terms of non collective or collective helix axis disorder are considered. and the a ppropriate powder-pattern limits are recovered. The H-2 NMR spectral l ine shapes have been calculated by using the Monte Carlo method, i.e., by randomly sampling over the static uniaxial distributions of the ba se pairs and helix axes. The results of the simulations and the struct ural parameters are in excellent agreement with X-ray diffraction stud ies, which indicate the presence of either the A-form or B-form of DNA under the given experimental conditions. Only a static distribution o f base pairs is needed to account for the spectral line shapes on the H-2 NMR time scale, whereas the effects of faster librational motions are contained in the Intrinsic line widths and the effective coupling constants. The present H-2 NMR approach can aid in developing a more c omprehensive picture of DNA conformation and dynamics as an adjunct to X-ray crystallography, fluorescence depolarization, and light-scatter ing methods, and moreover may prove useful in studies of protein-nucle ic acid interactions.