Charge-screening dominates signal transduction in electrochemical nucleic acid sensors for aminoglycosides

Abstract

Electrochemical aptamer-based (EAB) sensors have emerged as a promising framework for reagentless, real-time molecular monitoring in complex biological matrices. Signal transduction in a prominent benchmark system—targeting aminoglycoside antibiotics—has been nearly universally attributed to target-specific, binding-induced conformational changes that modulate the distance between a redox reporter and the electrode surface. Here, using a suite of interfacial electrochemical and optical characterization methods, we systematically show that charge-screening, not structure switching, dominates the signaling mechanism in the case of the aminoglycoside EAB sensor. First, we demonstrate that the legacy aminoglycoside sensor sequence exhibits apparent affinities and relative electron kinetic modulations similar to unrelated control sequences, including generic stem-loop hairpins, unstructured poly-T sequences, and short duplexes. Multi-modal validation via bio-layer interferometry (BLI), circular dichroism (CD), and fluorescence spectroscopy confirms that this promiscuous target association occurs across disparate DNA sequences and without detectable conformational reconfiguration. Further investigation via charge-scaling polyamine assays and on-electrode fluorescence imaging demonstrate that the dominant signal transduction mechanism in these sensors is instead driven by macro-scale electrostatic backbone charge-screening.