Controlled Sensing of User-Defined Aptamer-Based Targets Using Scanning Ionic Conductance Spectroscopy

Solid-state nanopores offer the possibility of detecting disease biomarkers in early diagnostic applications. Standard approaches harness fingerprinting, where protein targets are bound to DNA carriers and detected in free translocation with a solid-state nanopore. However, they suffer from several drawbacks, including uncontrolled fast translocations, which lead to low detection accuracy and a low signal-to-noise ratio (SNR). This has hampered their application in clinical settings. Here, we propose a nanopore-based system capable of sensing selected molecules of interest from biological fluids by harnessing programmable aptamer sequences attached to DNA carrier systems that are tethered to glass surfaces. This allows for spatial and velocity control over translocation in the x, y, and z directions and enables the repeated scanning of the same analyte. The scanning ion conductance spectroscopy (SICS) based approach distinguishes itself from standard nanopore-based approaches with its ability to repeatedly scan the same aptamer molecule target site more than 5 times. We designed a DNA carrier with multiple binding sites for different aptamers to increase the yield of the experiment. Our approach achieves a detection rate of up to 74%, significantly higher than the 14% achieved with standard solid-state nanopore measurements. The strong spatial control also allows for significantly increased densities of aptamer target sites along the same DNA carrier, thereby paving the way for multiplexed sensing. The system offers user-defined programmability with different aptamer sequences, potentially expanding the use of our system to sense other disease biomarkers.