Figure 6

Hydroxyl radical footprinting reveals the periodicity of the DNA around the histone core. Radiolabeled samples, both free duplex (labeled in blue) and nucleosomes (NCP, labeled in red) substrates, were exposed to hydroxyl radicals. Reactivity toward hydroxyl radical for the CGG-containing strands of the FMR1 substrates are shown in panel A. Reactions were performed on both free duplex (labeled in blue) and nucleosome (NCP, labeled in red) substrates. In panel A, lanes 1 contain FMR1-CGG19, lanes 2 contain FMR1-1AGGa, lanes 3 contain FMR1-1AGGb, and lanes 4 contain FMR1-2AGG. The marker lane consists of the Maxam-Gilbert A/G sequencing reaction performed on S1a. The location of the repeat tract and interruptions are indicated on the right-hand side of the gel. Panel B shows the reactivity at each nucleotide, generated from the gel presented in A. The arrows indicate the position of the A in the AGG interruptions.