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. Author manuscript; available in PMC: 2013 Aug 21.
Published in final edited form as: Biochemistry. 2000 Sep 19;39(37):11514–11522. doi: 10.1021/bi0010468

Figure 5. Hydroxyl Radical Autofootprinting of the Experimental Molecule Before Restriction.

Figure 5

Each of the junctions is shown, A, B, and C, moving from top to bottom. The appropriate residues are shown in a clockwise fashion as one proceeds around the junction; see the top of Figure 2 for strand numbering. Each panel contains two intensity traces, one for the indicated residues when incorporated into the double crossover (DX) and a second for the same strand when paired with its traditional Watson-Crick complement (DS). The two nucleotides that flank the junction are indicated by a pair of arrows, regardless of whether the nucleotides are designated to be on the crossover strands or on the helical strands. The helical strands are in the first and third panels, from left to right, and the crossover strands are in the second and fourth panels. In each case, the pattern at the junction is similar between the DX and DS molecules for the helical strands, but marked protection is visible on the crossover strands.