Figure 3.

Effect of arrest on the transcript arrangement in RNAP. (A) RNase A footprinting of the transcript in active EC²⁶ and in arrested EC²⁷. The RNA in the complexes was internally labeled at positions +26A or +12C. Each sample was treated with RNase A and fractionated by centrifugation into soluble (s) and matrix-associated (p) fractions before gel analysis. Sequences of the transcripts are shown alongside the autoradiograms, asterisks mark positions of labeling, and arrows show major cuts introduced into the RNA (bold shaded line) by RNase A. The cylinders represent the transcript segments protected by RNAP in the active and arrested complexes. Nonfractionated samples (t) are included as controls. (B) 5′-Terminal phosphorylation of the transcripts. RNA-labeled EC²⁰ and EC²⁷ (lanes 6 and 4) and arrested fraction of EC²⁷ purified by chase (lane 2) were treated with T4 polynucleotide kinase in the presence of ATP (lanes 5, 3, and 1). The symbol (P) indicates the phosphorylated transcripts. Arrows indicate the mobility of phosphorylated and nonphosphorylated transcripts.