Ion Fountain Nanopore Readers for High-Resolution DNA and RNA Sequencing

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Project Summary We propose to develop a new paradigm in nanopore-based sensing, involving ion-fountain nanopore readers (IFNRs). In these devices, a DNA or RNA molecule is moved through a sub-2-nm pore, and electronic sensing of the DNA sequence is made by recording the rate at which ions floss back and forth between the bulk and the very small volume of space within the membrane that contains the pore. A key component of the device is related to MXenes, two-dimensional layered materials that are electrically conductive, hydrophilic, and most importantly, intercalate various cations in the interstitial region between their sheets. We have recently developed a method for waferscale assembly of monolayer and bilayer MXene sheets in which MXene flakes spontaneously organize to a mosaic of electrically conductive large-area ordered films. By making a bilayer MXene film with a sub-2-nm diameter hole through it, we create an ion fountain that stores and releases ions by passing them through the pore opening. The main advantage of this type of a nanopore sensor is that access resistance is eliminated on one side of the pore, which beats fundamental resolution limits of conventional nanopore sensing. Another advantage of this type of a device is that a physically thicker pore can be fabricated while still exhibiting a resolution of an atomically-thin nanopore membrane. We are proposing here to develop the IFNR architecture, supplemental electronics measurement platform that allows DNA and RNA capture and readout, and software for basecalling. If successful, our devices will be able to read DNA/RNA faster than state-of-the-art technology (>1,000 bases per second) and further, detect at high accuracy various types of DNA and RNA base modifications.