FIG. 7.

DNase I footprinting analysis of the native SSO454-SRSR complexes. (A) SRSR-2p was sequenced (lanes 1 to 4) and footprinted (lanes 5 to 8). Lane 5, no protein; lanes 6, 7, and 8, a two-, four-, and sixfold molar excess of purified protein, respectively, was incubated with 30 ng of DNA, ³²P end labeled at the free 5′ end in the presence of 600 ng of pUC18 DNA, and digested with DNase I (see Materials and Methods). The positions of the two repeat units are indicated by brackets. (B) Both strands of SRSR-2c were sequenced (lanes 1 to 4) and footprinted (lanes 5 to 8). In the left gel, 72 ng of labeled DNA was complexed with no protein (lane 5) or with a 0.6-, 1.2-, or 2.4 molar protein-DNA ratio (lanes 6, 7, and 8, respectively). In the right gel, 36 ng of labeled DNA was incubated with no protein (lane 5) or with a 1.6- or 6.4-fold molar excess of protein (lanes 6 and 7, respectively). All of the footprinting samples were digested with DNase I in the presence of 600 ng of pUC18 DNA. Strongly enhanced DNase I cuts in panels A and B are indicated by arrows. (C) Data from panel B are superimposed on the secondary structure of SRSR-2c.