DNA STRUCTURE AND DYNAMICS IN BAMHI-DNA INTERACTIONS

Scripps College, Claremont CA

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Abstract

Recognition of specific DNA sequences by proteins plays an important role in many biological functions. Structural studies have shown that this specific recognition usually involves distortion of the DNA structure to accommodate protein binding. Two models for the mechanism of this specific recognition have emerged. In one, the protein plays an active role in recognition by rearranging itself and bending the DNA. It is suggested that the free energy released upon binding is sufficient to pay for that required for structural distortions. However, in order for complex formation to be favorable, the free energy required to bend the DNA and/or rearrange the protein must be low. Another model suggests that DNA possesses an intrinsic flexibility manifested in local, large amplitude dynamics. These flexible regions provide soft-spots which are easily distorted upon protein binding. In both these models, bending of the DNA must a low free energy process, suggesting that DNA has some inherent flexibility. In order to test this hypothesis, studies of local DNA dynamics must accompany structural investigations. In the next three years we plan to use high-resolution NMR studies and solid-state deuterium NMR studies to explore the local structural variations and dynamics of a DNA dodecamer containing the binding site for the BamHI restriction endonuclease. Specifically we propose the following program l) Synthesize deuterium labeled DNA phosphoramidites for incorporation into a DNA dodecamer containing the BamHI binding site. 2) Use solid-state deuterium NMR to characterize the local dynamics of backbone and sugar moieties of the individual nucleotides in the dodecamer. 3) Use high-resolution NMR to provide a structural description of the DNA dodecamer.