Non-equilibrium Dynamics of Ligase-Fueled DNA Solutions

Many cellular processes rely on DNA ligation, mediated by the enzyme ligase that anneals the ends of neighboring DNA strands to form longer strands. By elongating DNA chains, this enzymatic activity can introduce entanglements into unentangled solutions of DNA significantly slowing diffusion. However, circular DNA, which lacks free ends, is expected to be insensitive to ligase activity. At the same time ligation may introduce circular topologies by annealing the two ends of a single DNA chain. Here, using fluorescence microscopy, differential dynamic microscopy (DDM), and time-resolved gel electrophoresis, we investigate the role of molecular topology on ligation efficiency and how varying ligation rates map to time-varying DNA dynamics. Our results demonstrate that DNA diffusivity and chain growth dynamics are strongly affected by the topological state of DNA in ligase-fueled systems, allowing for a programmable switch to locally enhance or suppress activity. In future work we will integrate additional enzymes and photo-responsive molecules to enhance control of these topologically-active DNA solutions, which could serve as a platform for self-healing and self-mixing materials with applications from wound healing and infrastructure repair to responsive filtration and sequestration of toxins.