FIG. 3.

Roles of conserved adenines in repeat motifs (DR2 and DR1) of DR21 in PhoP-DNA interactions. (A) Sequence of the 23-bp core binding region comprising two direct repeat motifs (indicated in uppercase letters) with the DR2 site upstream of DR1 site, including the 5-bp intervening spacer region (indicated in lowercase letters) of the natural sequence. The nucleotides in both repeat motifs are numbered from 5′ to 3′ (at the bottom), and the conserved adenines are indicated by gray shadings. (B and C) EMSA of oligonucleotide-based DNA probes (∼20 nM) with various concentrations of PhoP using duplexes carrying the indicated substitutions at the A¹ (lanes 1 to 7) and A⁷ (lanes 8 to 14) positions of the DR2 (B) or DR1 motifs (C). Reaction condition was as described in Materials and Methods. Protein-DNA complexes were analyzed as described in the legend to Fig. 1A.