Continuous biosensing provides real-time information about biochemical processes and holds great potential for health monitoring. Aptamers have emerged as promising alternatives over traditional biorecognition elements. However, the underlying aptamer-target binding interactions are often poorly understood. Here, we present a technique that can decode aptamer-protein binding interactions at the single-molecule level. We demonstrate that our single-molecule assay is able to decode the underlying binding kinetics of aptamers despite their similar binding affinity. Guided by computational simulations and validated with quartz crystal microbalance experiments, we show that the quantitative insights generated by this single-molecule technique enabled the rational understanding of biosensor performance (i.e., the sensitivity and limit of detection). This capability was demonstrated with thrombin as the analyte and the structurally similar aptamers HD1, RE31, and NU172 as the biorecognition elements. This work decodes aptamer-protein interactions with high temporal resolution, paving the way for the rational design of aptamer-based biosensors.

Accurate and real-time monitoring of biomarker proteins, such as Tumor Necrosis Factor (TNF) alpha, plays a vital role in early disease diagnosis, effective treatment design, and personalized health management strategies. However, existing detection methods, including enzyme-linked immunosorbent assay (ELISA), radioimmune assays (RIA), and polymerase chain reaction (PCR), have significant drawbacks regarding sensitivity, cost, time, and labor efficiency, emphasizing the urgent need for alternative biosensing techniques. Here, we present a mass-based biosensing approach utilizing aptamers for the real-time detection of proteins, using TNF-alpha as the model analyte. The recognition process is based on the selective binding of the target molecule to the aptamer's unique three-dimensional structure. By utilizing a quartz crystal microbalance (QCM) as the transducing element, real-time detection of target binding is translated into a linear decrease in resonant frequency due to the change in mass upon target binding. The developed aptasensor enabled real-time quantification of TNF-alpha with high reliability, sensitivity, and specificity. The sensitivity of the sensor ranged from 14.5 nM to 115.6 nM, in which a linear correlation between target concentration and frequency decrease rate was found. Successful sensor regeneration demonstrated potential for continuous measurements in solution. By directly monitoring the change in mass during sensor fabrication and upon analyte binding, this platform provides key mechanistic insights in the surface functionalization process during sensor fabrication and analyte binding kinetics during sensor operation. In the future, incorporation of alternative target receptors, by simply changing the aptamer sequence, can broaden the analyte spectrum, making this platform highly versatile. We hereby demonstrate a technology that can be utilized for various biosensing platforms upon minimal modifications, including electrochemical and optical systems, for a wide range of macromolecular analytes.