Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings

The local structure of nucleic acids can be determined from traditional sol ution NMR techniques, but it is usually not possible to uniquely define the global conformation of DNA or RNA double helices. This results from the sh ort-range nature of the NOE-distance and torsion angle constraints used in generating the solution structures. However. new alignment techniques make it possible to readily measure residual dipolar couplings, which provide in formation on the relative orientation of individual bond vectors in the mol ecule. To determine the effects of incorporating dipolar couplings in the s tructure determinations of nucleic acids, molecular dynamics calculations w ere performed with simulated constraints derived from two DNA duplex target molecules. Refinements that included NOE, torsion angle, and dipolar coupl ing constraints were: compared to refinements without dipolar couplings. Th ese results show that dipolar couplings significantly improved the local st ructure while also dramatically improving the global structure of DNA duple xes. The model simulations also illustrate that molecular dynamics calculat ions induce changes in the local structure before the global structure, whi ch can have important implications for refinements with dipolar coupling co nstraints. Results are presented that show that the inclusion of dipolar co upling constraints makes it possible to accurately and precisely reproduce the overall helical bend in a DNA duplex. The implications of including dip olar coupling constraints in defining DNA global structure and DNA bending in solution will be discussed.