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

Abstract

The DNA-binding protein from starved cells (Dps) compacts bacterial DNA into stress-protective condensates, yet the physical mechanisms underlying this process and the material properties of the resulting condensates remain poorly understood. Here, we combine coarse-grained Brownian dynamics simulations with Flory-Huggins polymer theory to elucidate the structural, dynamic, and thermodynamic principles governing Dps:DNA organization and condensate formation. The simulations, in which DNA is represented as bead-spring polymers and Dps as spherical particles, reveal that weak Dps:DNA attraction and low Dps concentrations produce extended, network-like morphologies, whereas stronger interactions and higher Dps concentrations drive compaction into dense globular condensates with suppressed DNA mobility and sub-diffusive dynamics. Complementary Flory-Huggins analysis identifies the corresponding thermodynamic regimes and shows how Dps:DNA affinity, DNA:DNA and Dps:Dps repulsion, and solvent quality determine the boundaries between homogeneous and phase-separated states. Together, the two approaches provide a unified microscopic and thermodynamic picture of condensate formation, bridging molecular interactions with emergent mesoscale structures. These results advance understanding of protein-nucleic-acid phase behavior and illustrate general principles governing biomolecular condensation in soft matter systems.