Conformational analysis of DNA in complexes with Escherichia coli RNA polymerase: Modeling and experiments

The conformational behavior of T2 DNA upon its interaction with Escherichia coil RNA polymerase was studied using the spin label approach. The DNA was modified with an imidazolide spin label at the glucose hydroxyls of hydrox ymethylcytidines. It is shown that the attachment of RNA polymerase to DNA results in specific conformational changes in the latter only under conditi ons promoting formation of open promoter complexes. These changes affect no t only the promoters but also other regions in the template that do not dir ectly contact with the enzyme. The applicability of the known theoretical m odels of DNA dynamics to explaining this effect was analyzed.