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171386 https://hdl.handle.net/2286/R.2.N.171386 http://rightsstatements.org/vocab/InC/1.0/ All Rights Reserved 2022 2026-12-01T11:44:46 139 pages Doctoral Dissertation Academic theses Text eng Xia, Pengkun Wang, Chao CW Yu, Hongbin HY Christen, Jennifer Blain JBC Goryll, Michael MG Arizona State University Partial requirement for: Ph.D., Arizona State University, 2022 Field of study: Electrical Engineering Solid-state nanopore demonstrated great potential as a versatile and high-throughput single-molecule biosensor. However, the high capacitive noise of the conventionally used silicon substrates has seriously limited the recording bandwidth and thus the sensing accuracy. Different from recent efforts producing sub-10 pF nanopores which usually involve multiple techniques, complex manual processing, or expensive instrumentation, a new approach was proposed to form nanopore membranes on highly resistive sapphire to promote low-noise nanopore sensing using anisotropic sapphire etching with inexpensive etching setup in wafer-scale. In the first demonstration with a triangular window mask design, scalable formation of small (<300 µm2) intact membranes (small membrane capacitances, 0.6 pF) were created over 2-inch wafers. By innovating the window design to a hexagonal shape considering the hexagonal lattice structure of sapphire, sapphire facet competition serves to suppress the formation of more complex polygons but creates stable triangular membranes with their area insensitive to the facet alignment within 25 degrees wide range. Thus, a new scheme was proposed on a two-inch sapphire wafer to produce chips with an area of <30 μm2 for 81% chips, or an estimated membrane capacitance of about 0.06 pF. This approach further mitigates the membrane capacitances with proven reproducibility and uniformity over a wafer scale. Deoxyribonucleic Acid (DNA), an extremely informationally dense material, has great data storage and encryption potential. As a first demonstration, different from conventional slow characterization techniques, SaS nanopore as a fast and low-noise readout approach was used to characterize the nanotube-shaped origami with a data encryption layer for the first time. 96% four-helix bundle (4HB) – DNA multiway junction (WJ) events (114/119) on all the five spots of WJ were successfully read out without missing reading or overreading with a high signal-to-noise ratio (SNR) (from 8.2 for 2 × 3WJ to 18.7 for 2 × 6WJ). The individual events were further classified by a machine learning model for 2 × 3WJ and 2 × 6WJ, demonstrating a 92.9% correctly classified instances, indicating they were distinct enough in physical size for multilevel encoding. The demonstration proves the feasibility of high-capacity and high-security DNA data storage with efficient, high-resolution, and high-throughput readout by SaS nanopores. Electrical Engineering DNA data storage Low Noise Sapphire etching Single-molecule sensing Solid-state Nanopore Wafer-scale fabrication Sapphire-supported Nanopores for Low-noise Single-molecule Sensing