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bioRxiv · 10.64898/2025.11.28.691232

Emergent Morphologies, Slow Dynamics, and Phase Behavior in Dps:DNA assemblies

Alonso, A.·Mitra, S.·Studt, L.·Melcher, L.·Meyer, A. S.·Abbondanzieri, E. A.·Das, M.
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Abstract

The DNA-binding protein from starved cells (Dps) compacts bacterial DNA into stress-protective condensates, but the physical ingredients that are sufficient to produce the observed morphological and dynamical phenomenology remain unclear. Here we use Dps:DNA as the motivation for a broader soft-matter question: which properties govern the co-condensation of a semiflexible polymer with a binding co-solute, and how is the resulting condensate morphology selected? We combine coarse-grained Brownian dynamics (BD) simulations, in which DNA is a semiflexible bead-spring chain and Dps a spherical particle interacting through heterotypic attraction and homotypic repulsion, with a ternary Flory-Huggins free energy evolved under conserved Cahn-Hilliard-Cook dynamics. Both frameworks show that the condensate morphology is governed jointly by the heterotypic Dps:DNA attraction and by composition: attraction drives co-condensation, while at fixed attraction the relative abundance of the two species selects between extended, network-like structures and compact, droplet-like condensates. That two independent models, sampling different concentration regimes, both show composition-controlled morphology selection indicates it is a robust feature of the co-condensation thermodynamics. The simulations further reveal slow, heterogeneous dynamics: sub-diffusive Dps motion and a stretched-exponential collapse of chain dimensions, signatures of the dynamical arrest that accompanies compaction. The framework provides general, transferable principles for protein-nucleic-acid phase separation in soft and living matter.

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Alonso, A., Mitra, S., Studt, L., Melcher, L., Meyer, A. S., Abbondanzieri, E. A., Das, M.. 2025-12-02. Emergent Morphologies, Slow Dynamics, and Phase Behavior in Dps:DNA assemblies. https://doi.org/10.64898/2025.11.28.691232

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