Effects of sigma subunit and DNA template on the accessibility of rifamycin bound to RNA polymerase

Measurements of energy transfer in the rapid-diffusion limit from terbium complexes to rifamycin bound to E. coli RNA polymerase core and holoenzyme show that removal of the enzyme's sigma subunit markedly decreases the accessibility of bound rifamycin to small probe molecules in solution. Binding of holoenzyme to DNA also decreases the accessibility of enzymebound rifamycin. These results are consistent with the notion that rifamycin binds in a cleft on RNA polymerase which is held open by the sigma subunit, and which is involved in DNA binding. The use of D₂O buffers to improve experimental accuracy is also described.