Kinetics of segregation of topologically-modified ring polymers in cylindrical confinement

TL;DR

This study uses Langevin dynamics simulations to investigate how topological modifications, like loops, affect the segregation rate of ring polymers in cylindrical confinement, relevant to bacterial DNA behavior.

Contribution

It systematically analyzes the impact of loop number and length on segregation time, revealing that more loops generally decrease segregation time due to increased entropic repulsion.

Findings

Increasing the number of loops decreases segregation time.

Loop length and initial chain orientation influence segregation dynamics.

Entropic repulsion drives faster segregation with more loops.

Abstract

In Escherichia coli (E. coli), entropic repulsion between the two daughter DNA ring polymers under cylindrical confinement is believed to be an important factor governing chromosomal segregation. The repulsion can be enhanced by topological modifications, i.e., by the introduction of internal loops at certain locations along the contour of the circular DNA. However, the effect of topological modifications on the rate of segregation of ring polymers remains unclear. Therefore, we systematically varied the number and the contour length of loops introduced at selected locations by crosslinking monomers. The appropriate crosslinking was motivated by observations that extruded loops are located mainly near the origin of replication (ori-proximal) region of the E. coli chromosome. This resulted in the chains becoming intrinsically anisotropic. Using Langevin dynamics simulations of these topologically modified bead-spring polymers, we calculated the time required for segregation under cylinder confinement. With certain caveats, we found that increasing the number of loops resulted in a decrease in the time of segregation. In line with past work, we propose that this is due to the increase in the entropic repulsion between the polymers upon increasing the number of loops. In addition to the number of loops, the contour length of the loops and the mutual orientation of the (anisotropic) chains in the initial configurations played a role in determining the time of segregation.