The structure of the RNA polymerase-promoter complex. DNA-bending-angle by quantitative electrooptics

The complex formed between RNA polymerase holoenzyme from Escherichia coli and the strong promoter A1 from the phage T7 has been characterized by measurements of the electric dichroism. The dichroism decay time constant of a promoter DNA fragment with 126 bp increases upon binding of the polymerase, but the increase is less than expected for simple addition of the components at the known binding site. Our results demonstrate a protein-induced decrease of the hydrodynamic DNA dimensions, which is not a consistent with an increased flexibility, but indicates bending of the double helix with a relatively narrow distribution of bending angles. We have characterized the degree of DNA bending by bead model simulations and used, in addition to our present experimental data, the available information on the overall size and shape of the RNA polymerase, together with the location of the DNA bending center at the starting point of RNA synthesis. We conclude that the bending angle is 45 degrees (+/- 5 degrees).