Fig. 6.

Proposed model for transcriptional pausing by E. coli RNAP. TEC: Transcription Elongation Complex; the indices n−1, n, and n + 1 indicate the length of the RNA product. At pause sites, the paused state is rendered kinetically accessible to the polymerase through a slowing down of the on-pathway forward translocation rate. Depending on the sequence context, this paused state can transition slowly to a ≥ 2 bp backtracked state (in sites ‘a’ and ‘b’), be stabilized or destabilized by the nascent RNA (‘his’, ‘d’, and ‘P2’) or be stabilized by other mechanisms (such as in site ‘c’, which exhibited neither backtracking nor RNase sensitivity)