Date of Graduation

5-2022

Document Type

Thesis

Degree Name

Bachelor of Science

Degree Level

Undergraduate

Department

Mechanical Engineering

Advisor/Mentor

Tung, Cha-Hung Steve

Committee Member

Wejinya, Uchechukwu C.

Abstract

Sequencing DNA provides a positive impact for the biomedical community by understanding a wide variety of applications such as human genetics, disease, and pathogens. The reason the Arkansas Micro & Nano Systems lab is involved with research in DNA sequencing is due to the current, leading industry method. Nanopore sequencing was developed by Oxford Nanopore Technology in which its sequencing method separates double stranded DNA to electrically characterize individual nucleotides traveling through a charged nanopore. Unfortunately, nanopore sequencing uses biological materials that require a shelf life and drives high cost. Therefore, the Arkansas Micro & Nano Systems lab has developed a DNA sequencing method using atomic force microscopy (AFM) to eliminate any shelf life of materials. One of the main functions of sequencing DNA using atomic force microscopy is using force spectroscopy to control the movement of DNA by creating an electrostatic force between a cantilever tip and strand of DNA. Two different force spectroscopy methods were developed by graduate students, Dr. Bo Ma and Lucas Bartmann, to control DNA.

The focus of this report is to test and evaluate both spectroscopy methods developed by previous graduate students from the Arkansas Micro & Nano Systems lab and determine which procedure is more effective. Because atomic force microscopy will be used to control and move DNA, this undergraduate thesis will also entail a top-down approach of how to prepare DNA on a mica surface and how to use a CoreAFM in liquid mode to scan images of DNA. Explaining the procedure to locate DNA using an AFM and determining which spectroscopy method is more effective in moving DNA will hopefully provide a more efficient process of sequencing DNA using atomic force microscopy.

Keywords

DNA; DNA sequencing; human genetics; diseases; pathogens; nanopore; nanopore sequencing

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