Exosomes are nanoscale extracellular vesicles whose membrane-embedded proteins encode phenotypic information but remain difficult to interrogate due to hydrophobicity, low copy number, and nanoscale curvature. Here, we present AptEx-ID, a chemically guided aptamer evolution strategy that enables direct discovery and quantification of exosomal membrane proteins under native conditions. By introducing indole-modified nucleotides to emulate aromatic amino acid side chains, AptEx-ID expands the molecular interaction space of DNA, enhancing recognition of membrane-confined epitopes at the nano–bio interface. Integration of fluorescence-assisted microbead display with machine-learning–guided analysis enables target-agnostic probe evolution and multiplexed detection within a unified workflow. Applied to plasma-derived exosomes from hepatocellular carcinoma, AptEx-ID resolves a seven-aptamer membrane signature and identifies GTSE1 as a previously unrecognized exosomal surface protein associated with immunotherapy response. This work establishes chemically augmented nucleic acids as adaptive molecular materials for probing nanoscale biological membranes.
Cao et al. (Sat,) studied this question.