Figure 4.

(A) Increase of the −33 exonuclease III footprint signal in a combined DNA-binding assay. The presence of 1 μM 180–306 peptide with the 329–477 peptide (25 nM, 50 nM, 100 nM, 250 nM, 500 nM, and 1 μM) produced a significantly stronger signal compared with single peptide footprints. The 180–306 peptide was added to the assay mix before the 329–477 peptide. (B) Increase of the −33 exonuclease III footprint signal in a combined DNA-binding assay in the presence of 1 μM 180–306 peptide (+) and 1 μM 365–477 peptide. The peptides were premixed (25 μM) before addition of the DNA. The increased signal of the 365–477 peptide compared with the 329–477 peptide (Fig. 2) is attributable in part to reduced protection of the DNA fragment end. (C) Increase of the DNase I footprint signal in a combined assay containing the 329–477 peptide and 180–306 (lane 4) or 70–324 (lane 3) peptides each at 2 μM. The extent of protection was the same as for σ^N (lane 5). Peptides were premixed as in Fig. 2C before assay (lane 1, no protein). The 329–477 peptide was footprinted alone (4 μM) in lane 2 and protected the −24 part of the promoter weakly compared with the combined assays (lanes 3 and 4). Protected DNA sequences are bracketed.