Chromosome-like organization of an asymmetrical ring polymer confined in a cylindrical space

Abstract

To what extent does a confined polymer show chromosome-like organization? Using molecular dynamics simulations, we study a model Escherichia coli (E. coli) chromosome: an asymmetrical ring polymer, formed by small monomers on one side and big monomers on the other confined in a concentric-shell or simple cylinder with closed ends. The ring polymer is organized in the way observed for the E. coli chromosome: if the big monomers are assumed to be localized in the inner cylinder, the two “subchains” forming the ring are spontaneously partitioned in a parallel orientation with the “body” (big-monomer) chain linearly organized with a desired precision and the crossing (small-monomer) chain residing preferentially in the peripheral region. Furthermore, we show that the introduction of a “fluctuating boundary” between the two subchains leads to a double-peak distribution of ter-proximate loci, as seen in experiments, which would otherwise remain single-peaked. In a simple cylinder, however, a chromosome-like organization of the ring polymer typically requires an external mechanism such as cell-wall attachment. Finally, our results clarify to what degree the spatial organization of the chromosomes can be accomplished solely by ring asymmetry and anisotropic confinement.