Fig. 1.

Nucleotide addition cycle and alternative pausing pathways. The active site is depicted as semicircles with red RNA, black DNA, green NTP substrate, and yellow Mg²⁺ ions. Pausing might occur either by direct, reverse translocation of RNAP into backtrack states (pale yellow box; e.g., ref. 5) or isomerization of the active site into an inhibited conformation (squares) that could also facilitate backtracking (pale green box; e.g., ref. 4). Path 1 (pale green) and path 2 (pale blue) are alternative paths of isomerization that could occur before or during NTP binding, respectively.