Topological Gelation of Reconnecting Polymers

Bonato, A.; Marenduzzo, D.; Michieletto, D.; Orlandini, E.

doi:10.1101/2022.09.21.508941

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bioRxiv · 10.1101/2022.09.21.508941

Topological Gelation of Reconnecting Polymers

Bonato, A.·Marenduzzo, D.·Michieletto, D.·Orlandini, E.

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Abstract

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occur in a confined and highly entangled environment. Inspired by this observation, here we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realised using engineered DNA in presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems there is a topological gelation transition, which can be triggered by increasing either the stiffness or concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked and mixed loops, many of which are knotted. We predict the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilised container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids, e.g., DNA-based complex fluids or living polymer networks, with desired topologies.

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Bonato, A., Marenduzzo, D., Michieletto, D., Orlandini, E.. 2022-09-22. Topological Gelation of Reconnecting Polymers. https://doi.org/10.1101/2022.09.21.508941

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