The role of polymer architecture in the entropy driven segregation and spatial organization of bacterial chromosomes

Abstract

Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic segregation. Here we establish that `internal' loops within a modified-ring polymer architecture enhances entropic repulsion between two overlapping polymers confined in a cylinder. Moreover it also induces entropy-driven spatial organization of polymer segments as seen in-vivo. To that end, we design polymers of different architectures in our simulations, by introducing a minimal number of cross-links between particular monomers along the chain contour. This helps us to identify the underlying mechanisms which lead to faster segregation of spatially overlapping polymers as well as localization of specific polymer segments. The observed segregation dynamics of overlapping polymers is aided in our simulations by the frequent release of topological constraints, implemented by allowing chains to cross each at regular intervals. Additionally, we compare the segregation dynamics timescales with that of self-avoiding polymers and thereby highlight the significance of Topoisomerase in biological systems where DNA-strands are allowed to occasionally pass through each other. We use the blob model to provide a theoretical understanding of why or how certain architectures lead to enhanced entropic repulsive forces between loops, which in turn leads to the positional organization of segments relative to each other in confined environments. Lastly, we establish a correspondence between the C.crescentus bacterial species and our results for one particular polymer architecture.