Dynamic concatenation of ring DNA leads to non-equilibrium viscoelasticity tuned by DNA size and concentration.

Abstract

Topoisomerases can cleave, twist, untwist and reconnect ring DNA to enable diverse biological processes including DNA replication and repair, as well as the formation of concatenated structures such as kinetoplasts. At the same time, dense solutions of topologically-varying DNA have been shown to exhibit unique viscoelastic properties that can be tuned by DNA concentration, size and topology. Here, we use dynamic light scattering and particle-tracking microrheology to characterize the non-equilibrium viscoelastic properties of dense solutions of ring DNA undergoing dynamic concatenation via the linking and unlinking action of Topoisomerase II. We show that the frequency-dependent viscoelastic properties of these active Olympic ring hydrogels can be precisely tuned by varying the size and concentration of the DNA rings as well as the rate at which Topoisomerase II links and unlinks the DNA. Our work sheds new light on the oft overlooked role of varying viscoelasticity on biological processes that alter DNA topology, including the formation and restructuring of kinetoplasts, and the unwinding of DNA for replication and repair. Future work will build on this bio-inspired platform by incorporating additional enzymes that fragment and ligate DNA for in situ alteration of DNA length.