Morphology, Slow Dynamics, and Composition-Controlled Phase Behavior in a Minimal Model of Dps:DNA Co-Condensation

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.