The 9th International Conference on Multiscale Materials Modeling

講演情報

Symposium

H. Multiscale Mechanics of Polymers, Soft Matter and Network Materials

[SY-H8] Symposium H-8

2018年11月1日(木) 11:15 〜 12:30 Room9

Chair: Patrick R. Onck(Univ. of Groningen, Netherlands)

[SY-H8] Origin of large scale spatial organization of DNA-polymer in bacterial chromosomes.

Apratim Chatterji1, Tejal Agarwal2, Manjunath G.P.3, Farhat Habib4 (1.IISER-Pune, India 411008, India, 2.IISER-Pune, India, 411008, India, 3.NYU, USA, United States of America, 4.Inmobi, Bangalore, India 560103., India)

Using data from contact maps of the DNA-polymer of bacteria E. Coli (at kilo base pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a flexible ring polymer at very specific points along the chain. By suitable Monte Carlo Simulations we show that the presence of these cross-links lead to a specific 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 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 4642 kilo base pairs in a single chromosome. In our coarse grained flexible ring polymer model we used 4642 monomer beads and observe that around 82 cross links are enough to induce large scale organization of the molecule accounting for statistical fluctuations induced by thermal energy. The length of a DNA chain of a 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. We have carried out similar studies with the DNA-bacteria of C.Crecentus with cross-links at specific points relevant to the DNA of C.Crecentus, and obtain identical conclusions. This assures us about the robustness of our results.

Published in :
1. Tejal Agarwal et al J. Phys.: Condens. Matter 30 034003 (2018).
2. Tejal Agarwal, Tejal Agarwal et al EPL 121 18004 (2018).