Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings

Abstract

The local structure of nucleic acids can be determined from traditional solution NMR techniques, but it is usually not possible to uniquely define the global conformation of DNA or RNA double helices. This results from the short-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 information on the relative orientation of individual bond vectors in the molecule. To determine the effects of incorporating dipolar couplings in the structure determinations of nucleic acids, molecular dynamics calculations were performed with simulated constraints derived from two DNA duplex target molecules. Refinements that included NOE, torsion angle, and dipolar coupling constraints were compared to refinements without dipolar couplings. These results show that dipolar couplings significantly improved the local structure while also dramatically improving the global structure of DNA duplexes. The model simulations also illustrate that molecular dynamics calculations induce changes in the local structure before the global structure, which can have important implications for refinements with dipolar coupling constraints. Results are presented that show that the inclusion of dipolar coupling constraints makes it possible to accurately and precisely reproduce the overall helical bend in a DNA duplex. The implications of including dipolar coupling constraints in defining DNA global structure and DNA bending in solution will be discussed.

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

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Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

“…RDCs are particularly useful in nucleic acids, where the number of NOE restraints is typically relatively low, especially those involving long-range contacts. The fact that dipolar restraints provide information on internuclear bond vectors relative to a single axis system, that of the alignment tensor, allows for the study of global properties such as helix bending or relative helix orientations in multi-subunit molecules (Tjandra et al, 2000;Vermeulen et al, 2000;Al-Hashimi et al, 2002;Bondensgaard et al, 2002;MacDonald and Lu, 2002;Barbic et al, 2003;Lukavsky et al, 2003;Stefl et al, 2004). However, most applications have relied on a relatively small number of couplings per nucleotide, far fewer than the number of variable torsion angles.…”

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