Topological digestion drives time-varying rheology of entangled DNA fluids

TL;DR

This paper investigates how enzymatic topological modifications in DNA-based fluids induce time-dependent changes in rheological properties, combining experiments and simulations to reveal mechanisms and enable tunable viscosity behaviors.

Contribution

It introduces a novel approach using enzymatic reactions to control and study the time-varying rheology of entangled DNA fluids, demonstrating tunable viscosity changes.

Findings

Supercoiled to linear DNA conversion increases viscosity over time.

Fragmentation of linear DNA causes a universal decrease in viscosity.

Engineered DNA fluids can exhibit complex, tunable viscosity profiles.

Abstract

Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to constantly manipulate DNA topology, length, and structure. Inspired by this, here we engineer and study DNA-based complex fluids that undergo enzymatically-driven topological and architectural alterations via restriction endonuclease (RE) reactions. We show that these systems display time-dependent rheological properties that depend on the concentrations and properties of the comprising DNA and REs. Through time-resolved microrheology experiments and Brownian Dynamics simulations, we show that conversion of supercoiled to linear DNA topology leads to a monotonic increase in viscosity. On the other hand, the viscosity of entangled linear DNA undergoing fragmentation displays a universal decrease that we rationalize using living polymer theory. Finally, to showcase the tunability of these behaviours, we design a DNA fluid that exhibits a time-dependent increase, followed by a temporally-gated decrease, of its viscosity. Our results present a class of polymeric fluids that leverage naturally occurring enzymes to drive diverse time-varying rheology by performing architectural alterations to the constituents.