Date of Graduation

5-2023

Document Type

Thesis

Degree Name

Bachelor of Science in Mechanical Engineering

Degree Level

Undergraduate

Department

Mechanical Engineering

Advisor/Mentor

Tung, Cha-Hung Steve

Committee Member/Reader

Hu, Han

Abstract

An atomic force microscope (AFM) is used to scan high-resolution images on the nano scale. The lambda DNA used for this project are 48,502 base pairs in length and are double-stranded. This project utilizes the NanoSurf Core AFM in order to characterize and manipulate strands of lambda DNA which have been deposited on a mica surface. The deposition process of the DNA on the mica surface was developed by the National Institute of Standards and Technology and the University of Colorado - Boulder. The AFM is used in imaging mode to scan the mica surface to locate the DNA. When a linearized strand of DNA is identified, the AFM is then switched to spectroscopy mode which allows the user to attract the DNA strand to the cantilever tip. This electrostatic force between the DNA strand and cantilever tip enables the DNA to be moved to a location of the user’s choice. In the case of this research, the DNA needs to be moved approximately 1 millimeter into a graphene nanoribbon (GNR) sensor which will record the electromagnetic force exuded by the base pairs as they pass through the sensor. Each base pair corresponds to a different signal and can therefore be identified and sequenced by examining this signal. Previously, the NanoSurf Core AFM has been used to scan and lift off the DNA from the mica surface, however it has not been used to manipulate the DNA into the GNR sensor. The identified, successful process of lifting off the DNA was inefficient and needs to be optimized. After successful sequencing of the double-stranded lambda DNA, the next step will be to use the AFM to sequence single-stranded DNA. The objective of this research is to successfully imagine double-stranded Lambda and prove that spectroscopy can be used to lift the DNA strand off the prepared surface.

Keywords

Atomic Force Microscope; Lambda DNA; DNA Sequencing; AFM

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