Date Approved

1-27-2020

Embargo Period

1-28-2020

Document Type

Thesis

Degree Name

M.S. Biomedical Engineering

Department

Biomedical Engineering

College

Henry M. Rowan College of Engineering

First Advisor

Shim, Jiwook

Second Advisor

Byrne, Mark E.

Third Advisor

Beachley, Vincent Z.

Subject(s)

Biosensors; Nanopores

Disciplines

Biomedical Engineering and Bioengineering

Abstract

Solid-state nanopore based biosensors are cost effective, high-throughput engines for single molecule detection of biomolecules, which is useful for detecting epigenetic modifications on DNA; one of these being the potentially cancerous hypo, or hypermethylation of CpG islands. Despite its immense potential in the realm of disease diagnostics, nanopore detection as it stands faces various limitations that inhibit it from widespread commercial use. These include the complex method of solid-state nanopore fabrication, fast DNA translocations through the pore causing poor resolution, and poor signal to noise ratio. The following work aims to improve the efficacy of the solid-state nanopore biosensing platform as a disease diagnostic tool by improving ease of fabrication with automated MATLAB instrument control and controlled dielectric breakdown fabrication technique and increase signal resolution by using lithium chloride salt concentration gradients. In addition, methylated DNA labeled with certain methyl-binding proteins were tested in an attempt to localize areas of methylation on the DNA strand. These experiments yielded transport events that showed multilevel electrical signals that, in some instances, were able to distinguish between regions of bound protein and unbound DNA on the same strand. Increasing the accuracy of these multilevel event readings will aid in pinpointing localized regions of methylation on DNA and thereby increase the efficacy the solid-state nanopore platform for biosensing.

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