Figure 4

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, revealing a characteristic pattern of oscillating high and low reactivity as the DNA wraps around the histone core. Reactivity toward hydroxyl radical for the CGG-containing strands of the S1 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 the S1 control, lanes 2 contain S1-CGG19, lanes 3 contain S1-1AGGa, lanes 4 contain S1-1AGGb, and lanes 5 contain S1-2AGG. 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 dashed lines indicate the maxima of the S1 substrate and the arrows indicate the position of the A of the AGG interruptions.