Figure 1.

Properties of two classes of pause signals. (Top) Possible positions of the RNA 3′ nt during active elongation or pausing. Structures of class I and class II paused TECs are depicted with DNA (black) entering RNAP (blue) from downstream at right and separating near the active site (white circles). RNA (red) pairs with template DNA in an eight-bp hybrid (vertical red lines), then exits under the β flap domain (37). In the examples, the RNA nt in the hybrid (in the active state) are underlined. Nucleotide addition occurs when the RNA 3′ OH and template-specified NTP simultaneously occupy the left and right halves of RNAP's bipartite active site (i and i+1, respectively). At a class I pause, interaction of the pause hairpin with the β flap domain displaces the RNA 3′ OH away from the catalytic center. At a class II pause, RNAP enters pretranslocated or backtracked conformations (dashed red line). Backtracked RNA may enter the secondary channel through which NTPs are thought to enter (gray dotted outline; see refs. 37, 46, and 47). These structures are consistent with the tabulated differences in sensitivity to pyrophosphorolysis and transcript cleavage, effect of changes in hybrid stability on pausing, 5′ limit of positions at which antisense oligos can reduce pausing, effects of NusA and NusG, and effects of fast and slow RNAP mutants.