Molecular Footprints: Monitoring RNA Aptamer–Protein Interactions through Chemical modifications and Nanopore Readout

Proteins are key indicators of health and environmental changes, yet current detection methods rely on complex assays or costly equipment. This project explores a simplified, universal platform integrating chemical Kethoxal footprinting of RNA aptamers with Oxford Nanopore Technology. Kethoxal selectively modifies unprotected guanines, yielding distinct molecular footprints for bound and unbound aptamer-protein complexes. These footprints are identified in real time as the aptamers pass through the nanopore, creating unique electrical signals that directly report binding events without the need for immobilization or extensive sample processing. This method exploits aptamers’ high specificity, chemical stability, and broad target range to enable multiplexed protein quantification in almost any biofluid. If successful, it will transform proteomics with a portable, cost-effective, and single-molecule assay suitable for diagnostics, precision medicine, and environmental monitoring.