The chromosome of a bacterium consists of a mega-base pair long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike in eukaryotes, it lacks a nuclear membrane, and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modeling the chromosome simply as a circular polymer decorated with closed side-loops in a cylindrical confining volume, has been shown to already recapture some of the salient properties observed experimentally. Here, we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.

Springer Nature
R.T. Dame (Remus)
The Netherlands Organisation for Scientific Research (NWO)
Methods Mol. Biol.
Theory of Biomolecular Matter

Chaudhuri, D., & Mulder, B. (2018). Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome. In R. Dame (Ed.), Bacterial Chromatin: Methods and protocols (pp. 403–415). doi:10.1007/978-1-4939-8675-0_20