Synthetic oligo-DNA structures will be examined with 1H, 31P and 13C- nuclear magnetic resonance (NMR) to explore the variation of DNA dynamics upon changing the hydrogen-bonded structure. The molecules include examples of: (i) perfectly paired duplexes, (ii) a looped structure which varies the location and nature of the unpaired bases, and (iii) an antitumor-DNA drug complex. In order to accomplish these goals, a new isotope-labeling strategy is introduced that promises a low-cost procedure for creating oligomers ideally suited for 13C relaxation measurements. Refined three-dimensional structures will be obtained on the basis of nuclear Overhauser enhancement and J-correlation spectroscopic data. Measurements of NMR relaxation will help to establish the freedom of movement of the molecule about this average structure. The isotope labeling procedure also creates a good entry for three-dimensional NMR analysis of large DNA molecules interacting with proteins or other ligands. In the broad view, the experiments are designed to uncover mechanistic details in genetic regulation. This work will accelerate the recognition of the crucial determinants of three-dimensional DNA dynamics and structure that depend on sequence. It will also explore the interactions that may be important in understanding mechanisms for mutation and the effects of an intercalating antitumor drug. These studies will also contribute to a better understanding of the nature of overall and local motions in macromolecules.
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