Fig. 3.

Thymine glycol (Tg) exposure rates in 601 nucleosomes. ³²P-end-labeled 601 DNA containing a single Tg (DNA), and the same DNA after assembly into nucleosomes (NUC), were treated separately with varying concentrations of hNTH1, as outlined in Section 2. Aliquots from the reactions were collected, treated as described in the legend of Fig. 2, and fractionated on sequencing gels. Naked DNA reactions were used to computationally correct for small amounts of naked DNA contamination present in the nucleosome reactions as described previously [20]. The resulting excision data were normalized to the total naked DNA excised, were graphed as a function of time and fit to Eq. (1) (solid lines). The naked DNA and corrected nucleosome reaction progress curves are shown in the top panel. For added clarity, the bottom panel shows the same nucleosomal curves, graphed with an expanded vertical axis. The single kinetic constant for excision of Tg from 601 nucleosomes is consistent with a single conformational change and thus the single discrete translational position that 601 DNA adopts when assembled into nucleosomes.