Demonstration and structural basis of a therapeutic DNA aptamer for SARS-CoV-2 spike protein detection

Abstract

At the onset of the COVID-19 pandemic, the absence of a rapid and highly specific diagnostic method for the SARS-CoV-2 virus led to significant delays in detection, adversely affecting clinical outcomes. This shortfall highlights the urgent need for adaptable, scalable, and reusable diagnostic technologies to improve future pandemic responses. To address this challenge, we developed a renewable electrochemical impedance biosensor device employing a synthetic nucleotide-based therapeutic aptamer (termed aptasensor) targeting the SARS-CoV-2 spike (S) protein receptor-binding domain (RBD). We demonstrate that our aptasensor can detect the Omicron BA.2 S protein within one hour and possesses concentration-dependent sensitivity at biologically relevant levels. Notably, the aptasensor is reusable after regeneration by a simple pH 2 buffer treatment. Aptamer binding to the S protein was confirmed by immunogold labeling and visualization by negative-stain electron microscopy. We used cryogenic electron microscopy (cryo-EM) to resolve high-resolution maps of the S protein in both the open and closed conformations and characterized aptamer binding to the up RBD in the open conformation. Taken together, these results establish the versatility and scalability of aptamer-based biosensors, presenting them as a potential transformative diagnostic platform for emerging pathogens. This combination of rapid detection, specificity, and renewable capabilities in a single diagnostic solution marks a significant advance in pandemic preparedness.