FIG. 4.
The exoIII footprints of RNA polymerase II elongation complexes between positions +27 and +36 on the pML20-42 template. The sequence of the nontemplate DNA strand is shown at the bottom of each panel. Numbers in the left margins of both panels indicate distances downstream of the transcription start site. (A) U20 complexes were supplied with ATP, GTP, and CTP to stall polymerase at position +27; the C27 complexes were then gel filtered, treated with StuI, and advanced to the indicated positions by incubating with subset of NTPs. Front-edge boundaries were obtained as described in Materials and Methods. DNAs were resolved on a 6% polyacrylamide gel. The exoIII reactions on C27 complexes chased to the end of the template with all four NTPs are shown in lanes 14 to 16. The front edges of the more downstream conformations (see text) are marked by solid dots and the front edges of the more upstream conformations are indicated by open dots. Exact DNA markers are shown in lanes 17 to 20. (B) The rear-edge boundaries of RNA polymerase elongation complexes were obtained as just described, except that the DNA was labeled at the 5′ end of the template strand. DNAs were resolved on a 10% polyacrylamide gel.