Figure 5.

Initial transcription by RNAP proceeds through a scrunching mechanism. Reprinted from Kapanidis et al.69 with permission. (A) The three mechanistic models for initial transcription. Top, transient excursions; middle, inchworming; bottom, scrunching. (B) Schematic of the relative dye positions used in the experiments, and the corresponding FRET histograms comparing RPO to RPITC (FRET histogram: RPo is shown in the top panel, while RPITC is shown immediately beneath). TOP ROW: Since no change in FRET efficiency in going from RPO to RPITC for the upstream DNA‐RNAP trailing edge dye configuration, then the transient excursion model is ruled out. MIDDLE ROW: Since no change in FRET efficiency in going from RPO to RPITC for the spacer‐RNAP leading edge configuration, then the inchworming model was is ruled out (a change is expected if there was a flexible element in RNAP with the leading edge stretching into downstream DNA). BOTTOM ROW: The decreased FRET efficiency in going from RPO to RPITC for the spacer‐downstream DNA configuration supports the scrunching model for initial transcription mechanism.