Abstract
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.
Acknowledgements
The authors would like to express their gratitude to Professor Jinghui Wang for her invaluable support in coordinating the project and making its execution possible. We also thank Professor Guirong Wang for her generous assistance with clinical sample collection and transportation. Our appreciation extends to Dr. Wei Wang, Dr. Yu Liu, and Dr. Jinyuan Hu for their insightful advice on DAC modeling and computational simulations. This work was further supported by the instrumentation and technical expertise provided by Dr. Jiachang Huang and by the Instrumentation and Service Center for Science and Technology at Beijing Normal University.
Funding
The work was supported, in whole or in part, by the Guangdong Basic and Applied Basic Research Foundation (2025A1515011134) to Y.L. and by the Beijing Municipal Public Welfare Development and Reform Pilot Project for Medical Research Institutes (PWD&RPP-MRI, Grant Number JYY2023-14) to B.L.
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Liu, X., Zhang, T., Zhang, Q. et al. Divalent aptamer-mediated clustering for extracellular vesicle separation. Commun Biol (2026). https://doi.org/10.1038/s42003-026-10339-0
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DOI: https://doi.org/10.1038/s42003-026-10339-0
