Figure 1.

Structural features of designed 5′-dRP lesions and single nucleotide gaps in the nucleosome core particle (NCP). The color designation of the histones is shown at the top left and bottom. The template and lesion-containing strands of DNA are in cyan and magenta, respectively. Incorporation of dU within the nick at different locations allowed for strategic positioning of the lesions (red spheres) when reconstituted with the histone octamer so that they encompass the major structural parameters that regulate BER in the NCP: rotational and translational positioning of the DNA lesion. A total of four substrates containing either a 5′-dRP group or a single-nucleotide gap were used in this study: two outwardly oriented O (+10) and O (–35), one inwardly oriented I (–49), and a lesion with no definitive rotational orientation located only 13 nt from the DNA ends (–60). As shown in the diagram at the bottom, the central 60 bp are organized by the histone H3–H4 tetramer; whereas, the 30 nt on either side are in contact with the H2A-H2B heterodimer, and the remaining 13 nt are loosely associated with the histones. The difference in histone–DNA interactions in the central region vs. the ends gives rise to intrinsic differences in accessibility where regions bound by the H2B–H2A heterodimers are intrinsically more dynamic as described by others (47).