Table 1.

Calculations of predicted ΔG₃₇ of 9-bp RNA:DNA hybrid. RNA sequence comparison of wt and mutant templates upstream of the 3' end of RBT. Predicted ΔG₃₇ of RNA:DNA hybrid at pause sites and sites backtracked by 4- and 7-nt. The percentage of RBT for each template is shown. The pyrimidine-rich pause site (UUCU) and the upstream AU-rich (AAUUAU) sequence are outlined in blue, purine-rich (GAGAG) is in red. Gs to Us changes are in green. All sequences that were analyzed contain a UUCU sequence at the 3' end of the hybrid. The AU-rich sequence placed upstream of the hybrid does not alter backtracking from such a RNA:DNA hybrid. The GAGAG sequence strengthens the hybrid at the pause site in the wild type as an anti-pause element, promoting RNAP elongation. When a 5-bp is inserted between the GAGAG site and the pause site, RNAP backtracked from a weak hybrid to a stable hybrid, and hinders elongation.