Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation

The Journal of Chemical Physics
Ruggero CortiniMaria Barbi

Abstract

DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10(5)μm. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily d...Continue Reading

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Citations

Jan 28, 2016·Advances in Colloid and Interface Science·Panayotis Benetatos, YongSeok Jho
Feb 19, 2016·Soft Matter·Igor StankovićRené Messina
Feb 10, 2017·The Journal of Chemical Physics·C H M LimaE B Ramos
Jan 15, 2016·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Trinh X HoangAmos Maritan
Mar 30, 2017·Polymers·Wenyan XiaGuangcan Yang
Jul 28, 2020·Chemistry : a European Journal·Tania NevaJosé M García Fernández

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