Fig. 4. Footprinting of A. franciscana mitochondria reveals DNA-protein contacts. Footprints were detected in the termination region within tRNA_leu (C) and the control region (D), but no protein binding was detected immediately upstream of the 12S rRNA (A and B). For panels A and B, primers HSP1 and HSP2 were used for the heavy and light chains, respectively (see Table 1 for details). Panel C depicts primer extension of the light chain using the primer LEU 1, and panel D used the primer LSP 1 (genome positions numbered according to Valverde et al., 1994a). Lane assignments are as follows: panels A and B, 1, naked DNA; 2, in organello control (normoxia, pH 7.9); 3, in organello anoxia, pH 7.9; 4, in organello anoxia, pH 6.4; 5, normoxia, pH 6.4. Panels C and D: 1, normoxia, pH 6.4; 2, in organello anoxia, pH 6.4; 3, in organello anoxia, pH 7.9; 4, in organello control (normoxia, pH 7.9); 5, naked DNA. Relative to naked DNA, overmethylated residues are filled squares and undermethylated residues are unfilled squares.