Topological measurement of protein-induced DNA bend angles

A new method measures independently the changes in the DNA bend and winding angles that occur when a protein binds to its specific site in DNA. The procedure requires an investigation of the change in DNA topology induced when the protein binds to tandemly repeated sites of varying repeat length in circular DNA. This new method is superior to currently used methods because topology permits the measurements to be derived absolutely from first principles, and no comparison standards are required. The method is used to determine the bend and winding angles induced when catabolite gene activator protein binds to its site. The bend value obtained (69 +/- 4 degrees) is intermediate to those reported for two crystal forms of the complex.