Figure 6.

Slow intermediate mechanism. RNAP is depicted as in Fig. 1. At most template positions, fast translocation from the pretranslocated state to the active state allows tight NTP binding (assisted by a properly positioned 3′OH) and rapid transcription (top horizontal pathway)]. When RNAP encounters a pause, arrest, or termination site, it isomerizes to a slow intermediate in which the RNA 3′ end frays away from the DNA. A slight conformational opening of RNAP may precede and accelerate this change or may accompany it. Further rearrangement of the slow intermediate produces the different classes of paused, arrested, or terminating complexes. Escape of the slow intermediate back to the elongation pathway occurs by weak NTP binding and recapture of the 3′ OH in the active site. Amino acid substitutions in RNAP favor or disfavor the slow intermediate, whereas elongation factors NusA and NusG stabilize hairpin-RNAP interaction or inhibit backtracking, respectively, at later steps in the pathway. Whether termination sometimes involves hairpin-RNAP interaction (dotted line) and whether it occurs via hairpin-induced bubble collapse or RNA pull-out (18, 36) remains to be determined.