Fig. 5. (A) Halted (lanes 1 and 2) or paused (lanes 3 and 4) complexes containing transcripts internally labeled at +19 were formed on a template containing a non-functional class II element (lanes 1 and 2) or a functional class II template (lanes 3 and 4). Halting on the non-functional class II template was effected by incorporation of 3′-dCMP at +31. Peroxide and ascorbate were added to induce cleavage by the conjugate at residue 388 (lanes 2 and 4, labeled ‘+’). The transcript in the halted complex is cleaved 5 nt away from the 3′-end (lane 2), while in the paused complex it is cleaved 8 nt away. (B) Crystal structure of the T7RNAP EC with NT (non-template) strand, T (template) strand and residues 385, 388 colored as in Figure 2B. The –5 nt of the transcript is highlighted in yellow.