.lambda. Phage cro repressor interaction with its operator DNA: 2'-deoxy-5-fluorouracil OR3 analogs

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Abstract
The experiments here show that chemically synthesized DNA containing F at selected sites can be used to test specific predictions of a model for cro repressor-operator interaction. This is done by observation of the perturbation to the 19F NMR spectra of analogs of OR3 synthesized with 2''-deoxy-5-fluorouracil at specific positions in the DNA helix. Although the 3-dimensional structure of the cro repressor from phage .lambda. was previously determined by Matthews and co-workers, direct structural observations on the complex of the protein with its specific DNA recognition sequence, OR3, are limited. From that structure of the protein, alone, a model of its complex to DNA was previously built by fitting B-form DNA, with some distortion. That model proposes that the cro repressor contacts only 1 side of this DNA double helix and a number of specific protein-DNA contacts. To test the model, 2''-deoxy-5-fluorouracil was used to place the 19F nuclear spin-label on the side of the DNA contacting the cro repressor and on the opposite side facing away from the cro repressor. The results presented here are consistent with the prediction that .lambda. phage cro repressor contacts only 1 side of the DNA double helix.