Real-world modeling and simulation for the self-organized toroidal packing of a DNA chain

We performed experiments to elucidate the conformations of a single centimeter-sized bead chain through the mechanical vertical agitation under different crowding levels mediated by granular spheres. The bead chain adopted various conformations, such as a compact toroid, swelled toroid, rod-like shape, and random coil, depending on the solution conditions and experimental parameters like the crowding level and strength of the mechanical agitation. The characteristic conformations generated in macroscopic real-world experiments at several tens of centimeters exhibited similarity with those of a single giant double-stranded DNA chain above several tens of kilobase pairs, at several tens of micrometers, despite the significant difference in length scales. We performed Monte Carlo simulation and showed that the conformations of a semiflexible chain captured the essential structural features observed in the bead-chain experiment by adjusting the strength of vertical fluctuation and crowding level, suggesting general features of the semiflexible chain.