Fig. 4: From structural ensembles to kinking angle histograms.
From: Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level
a An ensemble of 1000 possible structures for the DNA was calculated (only 100 structures are shown in the figures for clarity, grey). From this ensemble, structures in agreement with the experimental FRET efficiencies were selected, i.e. 87 for free DNA (blue), 154 for DNA+F2 (magenta) and 199 for DNA+F1F2 (green). b Combined representation of the selected structures shown in a. All structures are aligned with respect to the 3′ stem. The axis of the 3′ stem is represented by a black line. The colored objects indicate the position of the tip of the 5′ stem for each selected structure (blue diamonds for free DNA; magenta circles for DNA+F2; green squares for DNA+F1F2). Two different views of the 3D plot are shown, a side view (top) and a view along the 3′ axis (bottom). c Kinking angle distributions for the selected structures shown in a. The mean and standard deviation of the angles are indicated for each histogram.
