DNA is a fundamental biomolecule in eukaryotic cells, playing central roles in processes ranging from genome organization and transcription to innate immune signaling. Recent studies have revealed that DNA can undergo protein-free phase separation in the presence of divalent cations, yet the underlying molecular mechanisms, including the interplay of base stacking, base pairing, electrostatics, and ion interactions, remain poorly understood. Here, we introduce an intermediate-resolution model for condensates of DNAs (iConDNA) that can capture key local and long-range structural features of dynamic DNAs and simulate their spontaneous phase transitions. By introducing explicit base stacking and pairing interactions, the iConDNA model not only reproduces major conformational properties of DNA homopolymers but also folds DNA hairpins and duplexes and captures their thermodynamic properties. With an effective model of explicit Mg2+, iConDNA successfully captures the temperature and magnesium concentration dependence of DNA properties. Together, these features enable iConDNA to qualitatively recapitulate homotypic DNA phase separation, providing a suitable tool to study DNA homotypic phase separation in biological and engineering applications.
The spatial distribution of small molecules within cells shapes their biological activity, yet these distributions are generally assumed to be governed passively by reaction-driven electrochemical gradients. Here we show that aminoglycoside antibiotics actively control their own subcellular organization by undergoing phase separation with RNAs. Combining in vitro reconstitution, bacterial assays, and molecular dynamics simulations, we discovered that aminoglycosides coacervate with RNA through multivalent electrostatic interactions, displacing and releasing RNA-bound Mg2+. This condensate-dependent Mg2+ release remodels the cytosolic labile Mg2+ pool and activates magnesium signaling. This effect dampens the magnesium-starvation regulation, sustains ribosome activity, and shifts the cellular electrochemical state, promoting bacterial fitness. Because condensation occurs only above a defined concentration threshold, it generates a non-monotonic dose-response in which higher antibiotic concentrations paradoxically enhance bacterial survival. This antibiotic condensate-dependent Mg2+ signaling confers tolerance to multiple ribosome-targeting antibiotics simultaneously even in cells lacking resistance gene, while condensate dissolution restores antibiotic efficacy. Our findings establish antibiotic-driven phase separation as a previously unrecognized mechanism to encode cellular signaling and identify antibiotic condensates as a distinct functional unit underlying drug tolerance.
Yuefeng Ma, Wen Yu, E. Moon et al.· bioRxiv· 0 citations
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