Relaxation Pathway of a Self-Entangled DNA Molecule Back to a Coil

Entanglements and knots continue to fascinated polymer and biophysicts due to their biological relevance, rheological implications and general complexity. While many theoretical studies and some simulations have been performed to study the relaxation of a collapsed, entangled polymer globule back to a random coil, experimental data has been quite elusive. In this work we present single molecule experiments that allow us to follow the relaxation pathway of an initially self-entangled DNA molecule back to an equilibrium coil. Single molecule fluorescence microscopy experiments allow us to demonstrate that the pathway back to equilibrium involves passing through two different metastable arrested conformation states. Importantly, we show strong evidence of intramolecular entanglements and the existence of knots. We also show a new route in the pathway that involves an end mediated nucleation event.  These results have broad importance in DNA separations and single molecule genomics, polymer rheology, and biomolecular nanotechnologies.