Actively induced supercoiling can slow down plasmid solutions by trapping the threading entanglements

arXiv:2506.22842v2 Announce Type: replace-cross
Abstract: Harnessing the topology of ring polymers as a design motif in functional nanomaterials is becoming a promising direction in the field of soft matter. For example, the ring topology of DNA plasmids prevents the relaxation of excess twist introduced to the polymer, instead resulting in helical supercoiled structures. In equilibrium semi-dilute solutions, tightly supercoiled rings relax faster than their torsionally relaxed counterparts, since the looser conformations of the latter allow for rings to thread through each other and entrain through entanglements. Here we use molecular simulations to explore a non-equilibrium scenario, in which a supercoiling agent, akin to gyrase enzymes, rapidly induces supercoiling in the suspensions of relaxed plasmids. The activity of the agent not only alters the conformational topology from open to branched, but also locks-in threaded rings into supramolecular clusters, which relax very slowly. Ultimately, our work shows how the polymer topology under non-equilibrium conditions can be leveraged to tune dynamic behavior of macromolecular systems, suggesting a method to create a class of driven materials glassified by activity.