Dynamics of DNA Knots during Chain Relaxation

Abstract

We perform single-molecule experiments and simulations to study the swelling of complex knots in linearly extended DNA molecules. We induce self-entanglement of DNA molecules in a microfluidic T-junction using an electrohydrodynamic instability and then stretch the molecules using divergent electric fields. After the chain is fully extended, the knot appears as a region of excess fluorescent brightness, and we shut off the field and observe the knot swelling over time. We find (1) the knot topologies created by the instability are more complex than what is expected from equilibrium simulations of knot formation, (2) the knot swells at a time scale comparable to the end-to-end relaxation of the chain, which indicates that the swelling is dictated by the chain’s global dynamics, and (3) knots are long-lived when the DNA is in the coiled state. These findings demonstrate the rich physics involved in the relaxation of knotted polymers which has not been examined heretofore.