UC Riverside

The capability to detect single molecules using nanopore sensors has rapidly gained prominence in developing next generation biosensors. Solid state nanopores have shown great potential in this field due to their unique features, including a robust structure, tunable size, and versatility, making them an attractive area of research. This thesis explores the electrokinetic effects for enhanced single molecule detection through nanopore sensing system. Specifically, we focus on investigating the electrophoretic force and electroosmotic flow to control the trajectory of biomolecules including DNA and proteins through the conical glass nanopores. The research study is divided into four specific aims, each targeting a specific aspect of nanopore sensing. The first chapter explains the theory of noise specifically high-frequency noise component in nanopore sensing systems. Then a straightforward approach is proposed to provide signal enhancement and improve the electrophoretic capture of DNA at the system level including the liquid-air interface. The second chapter seeks to explore diffusion limited capture mechanism of DNA under volumetric flow to propose a novel DNA quantification approach that eliminates external calibration requirement. The third chapter focuses on reducing the hydrodynamic forces to achieve high throughput and high-resolution DNA detection at low salt condition. Additionally, multi-pass DNA measurements is investigated under several factors including surface charge, permittivity, and voltage both experimentally and computationally. The last chapter explores DNA amplicons of sars-cov-2 viral genome in +10 electrolyte settings including symmetric and asymmetric conditions to quantify specificity of dCas9 binding to wild type and delta variant sequences using nanopore sensing system. This approach can provide an alternative to full genome DNA sequencing for highly sensitive and specific viral variant analysis with no antibodies or detection reagents requirement. Overall, this thesis provides new insights into the single molecular analysis of biological processes and reveals the potential of electrokinetic-based sensing for a broad range of applications, including biomolecular detection, disease diagnosis, and drug discovery. Furthermore, the ability to control and manipulate the transport of charged biomolecules using electrokinetic phenomena opens up new avenues for the design of advanced sensing platforms, with potential applications in areas such as point-of-care testing, and lab-on-a-chip devices.