(342h) Topology-Controlled Relaxation of Branched DNA Polymers

We report a combinatorial analysis of branched polymer relaxation using single molecule experiments, numerical methods, and simulations. In this work, we study graft-onto branched DNA polymers (asymmetric star, H, and comb polymers) following cessation of flow in tethered shear and planar extensional flow. We use single molecule fluorescence microscopy to characterize backbone chain relaxation from high stretch, and we present results for branched polymer relaxation as functions of time, branch frequency, and branch position. We compare results from experiments and Brownian dynamics simulations to a Rouse-inspired framework of relaxation modes for branched polymers.

Recently, we developed a new experimental system for single molecule studies of branched polymers based on graft-onto DNA. The vast majority of single polymer studies have relied on linear or circular DNA. We developed a biochemical synthesis platform for producing modularly branched DNA suitable for single polymer experiments. Our synthetic approach permits exact control over branch and backbone length, as well as relative control over branch frequency. In this way, our work has extended single polymer experiments to a new class of materials. Our results will provide a molecular-based understanding of the non-equilibrium dynamics of branched polymers, thereby enabling the development of advanced polymer processing methods.