Fig. 2.

Potassium permanganate (KMnO₄) footprints of RNAP–promoter complexes. Shown are representative results from KMnO₄ probing of complexes obtained early (20 sec, >70% I₁, <30% RP_o) and late (>2,500 sec, <5% I₁, >95% RP_o) in the time course of open complex formation at 17°C. G+A sequencing (40) and an uncut DNA control were performed. Positions of KMnO₄-reactive thymines in RP_o on the template strand are labeled. KMnO₄ reactivity observed in the 20 sec lanes in the presence and absence of heparin is consistent with the small population of RP_o complexes formed at this time after mixing. SI Table 3 quantifies the intensity of bands in this and two other independent experiments. See SI Fig. 7 and SI Table 3 for KMnO₄ probing of the nontemplate strand.