A Method for Direct Determination of Helical Parameters in Nucleic Acids Using Residual Dipolar Couplings

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Authors	TRANTÍREK Lukáš URBÁŠEK Milan ŠTEFL Richard FEIGON Juli SKLENÁŘ Vladimír
Year of publication	2000
Type	Article in Periodical
Magazine / Source	Journal of the American Chemical Society
MU Faculty or unit	Faculty of Science
Citation
Field	Biochemistry
Keywords	residual dipolar coupling; helical parameter; principal order frame; DNA; RNA; NMR; structure
Description	Helical parameters describing the base-stacking and base-pairing interactions in nucleic acids are not accessible directly from X-ray or NMR experimental data. Their values can be obtained only by the analysis of refined structures. This Communication presents a novel approach for direct determination of rotational helical parameters without a structure refinement. The METHADON (MEthod for deTermination of HelicAl parameters using Dipolar cOupliNgs) procedure is based on the Saupe order matrix analysis of at least five NMR residual dipolar couplings per base and takes advantage of the restricted mobility and rigid (and well-defined) geometry of purine and pyrimidine bases. The method is demonstrated on the DNA dodecamer d(CGCGAATTCGCG)
Related projects:	Laboratory of Structure and Dynamics of Biomolecules Biomolecular Structure-function Relationships and their role in the Metabolism