Predicting the Interfacial Energy and Morphology of DNA Condensates

The physics and morphology of biomolecular condensates formed via liquid–liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we develop a theoretical and computational framework to understand and predict multiphase morphologies in solutions of DNA nanostars. Since morphology is governed by interfacial energies between coexisting phases, we combine Flory–Huggins theory with coarse-grained molecular dynamics simulations to examine how these energies depend on key microscopic features of DNA nanostars, including size, valence, bending rigidity, Debye screening length, binding strength, and sticky-end distribution. The phase behavior of DNA nanostars is quantitatively captured by a generalized lattice model, where the interplay between sticky-end binding energy and conformational entropy determines the effective interactions. Focusing on condensates comprising two dense phases, we find that Janus-like morphologies are ubiquitous because the interfacial energies between the dense and dilute phases are typically comparable. In contrast, nested morphologies are rare, as they require a large asymmetry in the interfacial energies between the dense and dilute phases, which arises only for highly dissimilar nanostars, e.g., differing significantly in valence or size. Moreover, the interfacial energy between the two dense phases can be modulated either discretely by varying sticky-end types or continuously by tuning the crosslinker ratio, where the former may eliminate nested configurations. These findings establish physical design principles for constructing complex condensate architectures from microscopic molecular parameters.