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. Author manuscript; available in PMC: 2008 Sep 3.
Published in final edited form as: Biochemistry. 2006 Dec 19;45(51):15921–15930. doi: 10.1021/bi061626q

Figure 5.

Figure 5

Footprinting of XPA binding to the ds-ssDNA junctions in the Y-shape substrate with 3′- and 5′-ssDNA overhangs. Lanes 1-3, dsDNA footprinting by DNase I. Lanes 4 and 5, ssDNA footprinting by KMnO4. Y-shape substrates with 32P-labeled 5′-end of the bottom strand (indicated by the asterisk) were incubated at 30 °C for 15 min in binding buffer with or without XPA. After the incubation, substrates were digested with 0.7 ng DNase I (lanes 1-3) or probed with 0.2 mM KMnO4 (lanes 5 and 6), followed by hot piperidine treatment. Both footprinting reactions were performed at room temperature for 1 min. The samples were analyzed on a 12% denaturing polyacrylamide gel.