SUNY at Albany
June 19-23, 2001
New NMR Approaches for DNA Structure Determination
DNA structure determination by nuclear magnetic resonance (NMR) based methods is an under-restrained problem in general. Consequently, restrained molecular dynamics (rMD) has been widely used for NMR-based DNA structure calculations because the influence of the force-field assists in driving the DNA structure into a reasonable conformation. This is in contrast to the pure distance geometry (DG) methods that are widely used for protein structure determinations. However, the use of rMD introduces a dependence on the force-field used in the NMR-based DNA structure calculations. We show that when sparse NMR-based structural restraints are used, the force-field tends to outweigh the influence of the experimental restraints in terms of driving structures to converge. We demonstrate that significantly different structures can be obtained using AMBER and CHARMM force-fields. Methods have recently been introduced to incorporate 13C- and 15N-enriched synthetic DNA samples for NMR studies. This development is making it possible to apply many new NMR experimental techniques to the study of DNA structure and dynamics that are producing additional classes of restraints for DNA structure determinations. One important new class of structural restraint is the use of residual dipolar couplings to restrain both local and long-range structure in DNA. It will be shown that the use of residual dipolar couplings can be used to overcome the dependence of the convergence of NMR-based DNA structures on the force-field used in the rMD calculations.
This work has been supported by the U.S. Department of Energy's Office of Biological and Environmental Research under grant 22567 KP14-02-01-0.
Michael A. Kennedy
Environmental Molecular Sciences Laboratory, Pacific Northwest National
Laboratory, Richland, WA 99352