FIG. 2.

DNase I footprint analysis of polyamide 3 binding. (A) DNase I footprint of two upstream constructs, U+1 (lanes 1 to 10) and U−10 (lanes 11 to 20). Lanes 1 and 11, DNA alone; lanes 2 to 10 and 12 to 20, polyamide 3 at 1, 3, 5, 10, 15, 20, 30, 40, and 50 nM, respectively. The locations of the polyamide binding sites, TATA box, transcription start site (denoted +1), and direction of transcription (arrow) are indicated. The match site at −113 to −119 is also indicated. ³²P, end label on the DNA probe. (B) Graphical representation of polyamide 3 titration plotted as the fraction of DNA bound (normalized to the fraction bound in the absence of polyamide) versus polyamide concentration.