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. Author manuscript; available in PMC: 2010 Feb 10.
Published in final edited form as: Biochemistry. 2009 Feb 10;48(5):839–849. doi: 10.1021/bi801885w

Figure 8.

Figure 8

PAGE assay illustrating the recognition and photocleavage of mismatch and single base bulge recognition. Sequence contexts are listed along top line of each gel, and individual duplexes are indicated in the second line (M = matched, MM = mismatched, A = bulged adenine, C = cytosine, G = guanine, and T = thymine). In the top gel, the single strand beginning 5’-GAC CAG … (that containing the bulged base in SBB assemblies) is 5’-32P-labeled. In the bottom gel, the single strand beginning 5’-GAC TTA … is 5’-32P-labeled. In both experiments, 1 μM duplex was incubated with Rh(bpy)2(chrysi)3+ in 50 mM NaCl, 10 mM NaPi, pH 7.1. Samples were irradiated for 30 min on an Oriel Instruments solar simulator (320-440 nm emission) and incubated for 30 min at 60 °C prior to electrophoresis. “E” and “O” denote lanes containing even (10, 12, 14, 16) and odd (11, 13, 15, 17) standardization fragments.