Divalent aptamer-mediated clustering for extracellular vesicle separation

Extracellular vesicles (EVs) are important mediators of intercellular communication and promising sources of diagnostic and therapeutic biomarkers, yet effective EV isolation remains challenging due to trade-offs among yield, purity, and adaptability across biofluids. Here, we introduce divalent aptamer-mediated clustering (DAC), a streamlined affinity-based EV isolation strategy that induces controllable vesicle clustering and enables recovery by standard filtration. By exploiting multivalent aptamer binding to EV surface markers, DAC converts nanoscale vesicles into micron-scale clusters while preserving EV integrity and biological activity. We demonstrate robust EV isolation from plasma, urine, and cell culture media, and benchmark DAC against ultracentrifugation, density gradient ultracentrifugation, and size-exclusion chromatography. DAC achieves comparable or improved EV yield and purity with reduced processing time, cost, and operational complexity. Proteomic and metabolomic analyses show that DAC isolates affinity-defined EV subpopulations with cargo profiles distinct from those obtained using conventional methods. Moreover, DAC is readily adapted to alternative EV targets, exemplified by enrichment of EpCAM-positive EVs. Together, DAC provides a versatile and accessible platform for studying EV heterogeneity, function, and molecular composition. Divalent aptamers drive extracellular vesicle clustering to enable streamlined isolation of intact and functional EVs, offering a versatile platform for probing EV heterogeneity and biomolecular cargo.