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. 2011 May 27;39(16):7316–7328. doi: 10.1093/nar/gkr271

Figure 2.

Figure 2.

Mycobacterium tuberculosis UvrA binds preferentially to DNA intermediates containing single-stranded region. Reactions mixtures contained 250 pM of the indicated 32P-labelled substrate in the absence (lane 1) or presence of 1, 2.5, 5, 7.5, 10, 12.5, 15, 20, 25, 30 or 35 nM MtUvrA (lanes 2–12), respectively. The filled triangle on top of each gel image represents increasing concentrations of MtUvrA; in a to g panels the black arrowhead points to free-DNA and the squared bracket indicates MtUvrA–DNA complexes. Panels: a, single-stranded DNA (ODN1); b, non-damaged duplex DNA (ODN1 annealed to ODN6); c, damaged duplex DNA (ODN7 annealed to ODN8); d, 5′-overhang (ODN1 annealed to ODN5); e, flayed duplex DNA (ODN1 annealed to ODN4); f, 5′-flap (ODN1, ODN4 annealed to ODN5); g, bubble duplex (ODN2 annealed to ODN3) (for ODNs sequence see Supplementary Table S1). In panel h, the percentage of MtUvrA–DNA complex formation in panels a–c is plotted against the indicated amounts MtUvrA. In panel i, the percentage of MtUvrA–DNA complex formation in panel a and panels d to g is plotted against the indicated amounts MtUvrA. (filled circle), MtUvrA-single-stranded DNA; (filled square), MtUvrA-5′-overhang; (filled diamond), MtUvrA-flayed duplex DNA; (open square), MtUvrA-5′-flap; (open diamond), MtUvrA-bubble duplex DNA; (filled triangle), MtUvrA-non-damaged duplex DNA; (filled inverted triangle), MtUvrA-damaged duplex DNA. Each point on the curves represents the mean of three separate experiments. The best-fit curve was obtained by subjecting the data sets to non-linear regression analysis, in GraphPad PRISM (ver5.00), using the equation for one site specific binding with Hill slope.