Evolution of Aptamer Materials Maps Exosomal Surface Proteins at the Nano–Bio Interface

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.