The complex organization of DNA within bacteria, where megabase pairs of DNA are packed into a small volume, results from the interplay between biological factors and polymer physics. Inspired by the loop extrusion mechanism, we present simulation data for a “loops on a ring” model consisting of a ring backbone and grafting side loops, elucidating the mechanisms behind the spontaneous helicity of E. coli and C. crescentus chromosomes from a polymer physics perspective. We will present molecular dynamics (MD) results on the impact of the side loop packing on the helical structure of backbone, maintaining a consistent monomer density to mimic the DNA concentration in vivo while varying the size and distribution of side loops along a backbone of specific length under cylindrical confinement. The helicity quality is quantitatively measured and observed to change with confining dimensions and number of loops. For the parameters that deviate from the bottlebrush polymer limit, the grafts are either uniformly ( u ) or asymmetrically ( a ) distributed. At the same set of parameters, the u and a models can result in the structural organization of double helix and single helix, respectively, and the corresponding predicted contact maps are consistent with the experimental observations of C. crescentus and E. coli cells. Our results reveal how polymer physics contributes to the structural maintenance of chromosomes and provide insights into the self-assembly of confined grafting polymers.
Li Li (2026) studied this question.