Fig. 4: Theoretical description and simulation of DNA nanotube rings.
From: Triggered contraction of self-assembled micron-scale DNA nanotube rings
a Schematic illustration of the theory model representing the associated parameters. The DNA nanotubes are drawn as a continuous line and colored to distinguish surface (red) and interior (yellow) of the ring. The diameter of the bundle cross section is assumed to be negligible compared to the ring diameter D. Zoom: A discretized bead-spring representation of the DNA nanotubes is used in the MD simulations with parameters as indicated. b Snapshots of an isotropic initialization (left) and a DNA nanotube ring (right) taken from MD simulations. For clarity, the DNA nanotubes widths are increased. The cubic boxes show the simulation volume. c Coarse-grained MD simulation of the DNA ring formation from a solution of DNA nanotubes represented as bead-spring polymers. Individual nanotubes involved in ring formation are colored for clarity. A reduced persistence length is employed to facilitate the ring closure. d Kinetically trapped structure in incomplete ring formation after simulated annealing (right) (starting at temperature T1 (left) and annealing to a high temperature T2 = 8T1). e Transmission electron microscopy image of a kinetically trapped DNA ring as observed in experiments. Scale bar: 500 nm.
