Abstract
The interaction of λ cro represser with DNA is probed using synthetic 17 base-pair O R3 operators in which 5-fluorodeoxyuridine has been systematically incorporated at each of the nine positions normally occupied by a thymidine residue. By monitoring changes in chemical shift of the fluorine resonances upon cro represser binding in aqueous buffers of varying 2H 2O content, we have examined the specific cro repressor-O R3 DNA complex in detail. The results are interpreted in the context of the popular model for cro repressor-O R3 complex derived from the three-dimensional structure of the cro repressor in the absence of DNA. The results presented here not originally predicted by the model are: (1) there is an asymmetry in the environment at the two ends of the operator, although the base-pairs involved and the cro repressor dimer are symmetric; (2) there appears to be distortion of the DNA helix at two distinct positions; (3) changes of the DNA environment in the middle of the helix suggest additional DNA distortion not near the contact areas proposed in the model.
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