Universal Nanopore Sensor for Amplification-Free and Label-Free Detection of Molecular Biomarkers

Molecular diagnostics of biomarkers derived from tissues and bodily fluids are developing into a cornerstone of medical testing and potentially the foundation of a personalized medicine approach. Therefore, there is a need for universal biosensors capable of detecting different biomarker types with high performance and minimal complexity, ideally suitable for point-of-care use. Here, we present an integrated nanopore sensor for amplification-free, label-free, and quantitative detection of both proteins and nucleic acids from clinical samples. High performance is enabled by trapping target-carrying microbeads at the nanopore location and rapid detection of individual targets upon release from the beads. Low complexity is achieved via a simple solid-phase extraction protocol and optics-free, flow-based bead trapping. The device is validated through the analysis of biofluids from a baboon infected with SARS-CoV-2. Detection of the spike protein down to 100 fg/mL, with a linear count over 5 orders of magnitude, and SARS-CoV-2 RNA over the entire course of infection, down to a concentration of 7.5 aM, are demonstrated. This platform enables ultrasensitive, quantitative analysis of different biomarker types using a single protocol and holds promise as a universal biosensor for infectious disease detection and a wide range of applications.