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. 2018 Nov 17;115(12):2310–2326. doi: 10.1016/j.bpj.2018.11.015

Figure 4.

Figure 4

Two-well analysis of the TBP-DNA-NC2 dynamics. The results of a two-well analysis of the TBP-DNA-NC2 data are shown for the (a) 70-bp upstream-labeled AdML promoter DNA (DNA 1) and (b) the 80-bp upstream-labeled H2B promoter DNA (DNA 3). Left panels: Frame-wise spFRET histograms are shown for the respective measurements. Two dominant populations are observed, and the equilibrium coefficient can be estimated by fitting to the two populations to Gaussian distributions. Middle and right panels: from the two-state HMM analysis, the duration of each state before undergoing a transition was calculated from the Viterbi path determined for each trace from the parameters of the global HMM. The survival probability was fit to an exponential function (solid line, red). In addition, the rates from the HMM are shown (dashed line, blue). The given equilibrium coefficients are determined from the ratio of the rates determined from the HMM analysis. To see this figure in color, go online.