[C11] Biophysics

[C11-04] DNA knot dynamics under tension and confinement

*Souradeep Sengupta¹, Somendra Mohan Bhattacharjee¹, Garima Mishra¹ (1. Ashoka University (India))

Keywords:

DNA knots,topology,statistical physics,Brownian dynamics

Any sufficiently long object, if confined in a small enough environment, will tend to develop knots. Even though DNA is a very stiff polymer at short length-scales, its enormous length (and tight nuclear confinement) in many organisms makes the formation of knotted structures ubiquitous. The presence of these knots can play important roles in the regulation of various biological processes like translocation, replication, transcription and recombination, as well as in new-age genetic technologies like nanopore sequencing. Experiments have found that single knots in a DNA chain held fixed at the two ends behaved like localized random walkers undergoing near-diffusive motion, while computational studies have shown that this diffusive motion is dependent on chain stiffness, external tension and knot complexity. We develop a minimal computational model of wall-confined and tethered knotted DNA chains and find that this end-confinement replicates the effect of stiffness on the motion of a DNA knot, even without any local bending energy, with different regimes of knot dynamics from jammed to diffusive depending on induced chain tension. We also find that further confinement within boxes of decreasing size has a non-trivial and regime-dependent effect on knot motion. We also present some results from double-knotted chains and show that their entangled behaviour is also strongly affected by chain tension and confinement.

Refs:
1. Bao, Lee, Quake. “Behavior of Complex Knots in Single DNA Molecules”. Phys. Rev. Lett. 91, 265506. doi:10.1103/PhysRevLett.91.265506
2. Huang, Makarov. "Langevin Dynamics Simulations of the Diffusion of Molecular Knots in Tensioned Polymer Chains." J. Phys. Chem. A 2007, 111, 41, 10338–10344