Double helical chromosomes: a "loops on a ring" polymeric model

As one of the most important natural polymers, DNA has attracted significant interest over the past decades, particularly regarding its multiscale helical structures. The complex organization of DNA within the prokaryotic cell, where megabase pairs of DNA are packed into a limited space, results from the interplay between biological factors and polymer physics. In the bacterium E. coli, for example, the 1.5 mm long circular chromosome is confined within a cylindrical nucleoid of approximately 0.8 mm in diameter (D) and 2–4 mm in length (H). Inspired by the loop extrusion mechanism, we propose the "loops on a ring" model as an effective model of the structural organization of E. coli chromosomes, elucidating the mechanisms behind the spontaneous helicity from a polymer physics perspective. We will present molecular dynamics (MD) results on the impact of the distribution of side loops on the helical structure of backbone, maintaining a consistent packing fraction of total monomers to mimic the concentration of natural DNA in vivo while varying the distribution of side loops along a backbone of specific length. The results are summarized as a phase diagram for the helicity with respect to confining dimensions and loop distribution. The optimal dimensional ratio of the cylindrical volume to produce a helical conformation is D/H = 1/3, which closely matches the typical dimensions of E. coli cells. Through energetic and geometrical analysis, our results reveal how polymer physics contributes to the structural maintenance of chromosomes and provide insights into the self-assembly of confined bottlebrush polymers.