Fig. 6

3DOM imaging of λ-DNA labeled with SYTOX Orange. a 3DOM images (\(\rho\) component) of λ-DNA strands with color coding based on the average azimuthal orientation of the dye molecules measured within 65 nm voxels. b Visualization of orientation measurements along a short strand of λ-DNA in x-y and y-z views (gray box in (a)). The rods point in the direction of \(\rho\) and color-coded to denote \(\eta\). c pSIM images of λ-DNA, consistent with 3DOM results. d SYTOX Orange has an intercalation binding mode in DNA with an absorption dipole moment perpendicular to the DNA axis. e Histograms of orientation measurements along the DNA axis (yellow dash box in (a)). f Comparing 3DOM, pSIM and Widefield resolutions (white arrows in (a)). g Super-resolution images of λ-DNA strands exhibiting “bends”. h Zoom in on the x-y view of the boxed regions in (g). i Kinks formation occurs in DNA axis bending and the orientation of the visualized dye molecules changes (see arrows). j Possible state models for the localized structure of bending DNA. Scale bars (a, c), 5 μm; (b, g), 2 μm; (h, i), 500 nm