A high-throughput, flow cytometry approach to measure phase behavior and exchange in biomolecular condensates

Biomolecular condensates are essential for cellular organization, yet their formation dynamics and molecular content exchange properties remain poorly understood. Here we show that flow cytometry provides a high-throughput, solution-based platform for analyzing condensate behavior at the single-droplet level. Using self-interacting NPM1 condensates as a model, we demonstrate that this approach quantifies phase behavior across protein and salt conditions, measures the partitioning of diverse macromolecules-including antibodies, lipids, small-molecule drugs, and RNA-and detects molecular colocalization with high statistical precision. Importantly, we establish a high-throughput assay to track real-time molecular exchange between preformed condensates and newly added, orthogonally tagged protein. These measurements reveal that condensate aging significantly reduces molecular dynamisms, likely due to altered biophysical properties with time. Compared to conventional imaging techniques that require surface immobilization or complex instrumentation, our method enables rapid, quantitative characterization of condensate dynamics and molecular content, providing a scalable framework for probing condensate function.