Our objective is a detailed understanding of those factors which determine the structure and flexural rigidity of DNA. Over the past several years, the phenomenon of stable, sequence-dependent curvature of DNA has become widely recognized. DNA restriction fragments displaying apparent curvature (as manifested by reduced electrophoretic mobility) have been found in bacteria as well as in higher organisms. Moreover, evidence exists which intimates the functional significance of such curvature. However, the precise relationship between sequence and curvature, as well as the magnitude of the curvature itself, remain undetermined. We have begun a systematic, quantitative examination of sequence-directed curvature; the extension of these studies constitutes the primary aim of this proposal. We also wish to examine the suggestion that the 5'-TA-3' transition constitutes a point of significant flexibility in duplex DNA. In addition, we plan to complete our study of the magnitude of the distortion of the helix axis which results from the interstrand cross-linking of DNA by psoralens. Finally, we intend to continue our studies of the geometry of four-way DNA junctions, thought to be intermediates in the process of genetic recombination. Our studies will exploit two sensitive techniques, namely, (1) differential decay of birefringence and (2) measurements of the races of ligase-catalyzed cyclization of small DNA molecules. Both of these methods have undergone extensive development in our laboratory. Furthermore, we will utilize our existing computational models for both rotational diffusion and DNA cyclization in order to provide a sound, quantitative basis four the intepretation of our experimental results.
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