Role of special cross-links in structure formation of bacterial DNA polymer

Abstract

Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. By suitable Monte Carlo Simulations, we show that the presence of these cross-links leads to a particular architecture and organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of $E. Coli$ bacteria which has around $4.6$ million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used $4642$ monomer beads and observed that around $80$ cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain of an even simple bacterial cell such as $E. Coli$ is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify large scale structure of a polymer chain with a few cross-links.