Figure 4.

Effects of DNA bending on the B–Z transitions of methylated (indicated by m⁵) DNAs. (a) DNA sequences used for the B–Z transition experiments. Methylated cytosines are indicated in brown color. (b) FRET histograms of m⁵ B–Z linear and m⁵ BZ29-S19 samples at various concentrations of MgCl₂ obtained by the ALEX method. Histograms were fitted to a single Gaussian distribution. The black dotted lines denote the E of each sample in the absence of MgCl₂. The red dotted lines denote the E of each sample at the highest concentration of MgCl₂ (300 mM for m⁵ B–Z linear and 100 mM for m⁵ BZ29-S19). (c) E of m⁵ B–Z linear and m⁵ BZ29-S19 samples plotted against the concentration of MgCl₂. The blue dotted line denotes the midpoint of the m⁵ B–Z linear sample (78 mM), and the red dotted line denotes the midpoint of the m⁵ BZ29-S19 sample (2.8 mM). The inset graph shows the E values of the m⁵ BZ29-S19 sample at low salt concentrations. Error bars were obtained from three independent measurements. (d) B–Z transition midpoints of each sample (B–Z linear, BZ29-S19, m⁵ B–Z linear, and m⁵ BZ29-S19). The midpoints of the B–Z linear and BZ29-S19 samples were obtained from Figure 3c. As the bending force increases, the midpoint decreases. Error bars were obtained from three independent measurements.