Fig. 1: Structural and dynamic diversity in supercoiled DNA minicircles.

a–d High-resolution AFM images of natively supercoiled (σ = 0.03–0.06) DNA minicircles of 251 bp (a) and 339 bp (b–d) showing their helical structure and disruptions of canonical B-form DNA (marked by red arrowheads), where the angle of the helix changes rapidly, or where the DNA appears thinner or disrupted. Aspect ratios for each molecule: 048 (a), 0.44 (b bottom), 0.87 (b top), 0.78 (c) and 0.65 (d). e MD snapshots of minicircle conformations for 251 (first image) and 339 bp corresponding to the minicircles in the AFM images selected by visual inspection from explicitly solvated simulations (first, second and third images at ΔLk −1, 0 and −2, respectively) and from implicitly solvated simulations (fourth and fifth image) at ΔLk = 0. Top and side views (top and bottom row, respectively) show the degree of planarity of the depicted structures, where top refers to the top view of adsorbed DNA minicircles, and side the perpendicular plane. White and red lines indicate plectonemic loops of 9 and 6.5 nm width, respectively (see ‘Methods’). Aspect ratios are 0.45 ± 0.04, 0.30 ± 0.03, 0.86 ± 0.01, 0.81 ± 0.01 and 0.69 ± 0.01. f Time-lapse AFM measurements of a natively supercoiled 339 bp DNA minicircle, recorded at 3 min/frame. Fast scan direction is shown by white arrows. g Chronological snapshots from simulations of 500 ps duration for a 339 bp minicircle with ΔLk = −1 (see Supplementary Videos 6 and 7). Scale bars (inset): 10 nm and height scale (inset, d): 2.5 nm for all AFM images.