Self-Healing Biomaterials: Entangled DNA Networks

Abstract

The material that the cell uses to store genetic information actually becomes self-healing material when it must be segregated, transported across the length of the cell even in the face of its entanglements with itself, or condensed to prepare for this large scale transport. This is a naturally-occuring soft material that is capable of self-repair. Moreover, there is evidence that the material first senses the possibility of a stress-inducing, potentially fatal (to genome stability) topological entanglement, and quickly fortifies itself to limit or prevent the damage. The issue of how topology is conserved (controlled) by this type of biomaterial is itself an interesting mystery. I will present our experimental results using a bottom-up design approach, borrowing the naturally-occurring materials from the cell to study the design principles of this behavior. We incorporated micron-sized particles in lambda-DNA entangled networks in the presence of the topoisomerase II motor that performs the strand passage, at controllable ratio of enzyme units per average DNA entanglement and ATP concentration. We used bright-field microscopy to directly track the movement of the particles, which couple to the DNA fluctuating movement. Our observed scaling behavior suggests entangled dynamics in the bare DNA system, and nonentangled Rouse dynamics, with enzyme performing topological constraint relaxation, in the DNA+topo II + ATP system. These very time-dependent scaling behaviors are all predicted theoretically for entangled polymers with inclusion of a constrained release process in the case of presence of active topo II. The material self-heals to such a degree that, at saturating topoisomerase II motor and ATP concentrations, the long DNA polymer molecules do not even “feel” one another despite being entangled. We compare our experimental results to predictions of the constraint release model, measuring the “healing rate” at different dynamical length scales.