# Entropic elasticity and dynamics of the bacterial chromosome: a simulation study

## TL;DR

This simulation study investigates the mechanical response and dynamics of bacterial-like DNA polymers interacting with proteins, revealing how protein interactions influence force-extension behavior and DNA expansion after compression.

## Contribution

It introduces a detailed simulation model of bacterial DNA with proteins, highlighting the effects of steric interactions, protein binding, and supercoiling on DNA mechanics and kinetics.

## Key findings

- Non-DNA-binding proteins exert significant osmotic forces.
- Protein concentration affects DNA expansion dynamics.
- Intermediate protein-DNA interactions cause slow unzipping during expansion.

## Abstract

We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston" - a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein size, and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration, and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.