Date of Graduation

5-2024

Document Type

Thesis

Degree Name

Master of Science in Mechanical Engineering (MSME)

Degree Level

Graduate

Department

Mechanical Engineering

Advisor/Mentor

Steve Tung

Committee Member

Jin-Woo Kim

Second Committee Member

Uche Wejinya

Keywords

Carbon Nanotube; DNA; DNA Sequencing; MEMS

Abstract

DNA sequencing is of major importance as it is used in fields such as species differentiation, personalized medicine and food safety. Currently sequencing by synthesis is the most popular commercial method of sequencing DNA while Oxford nanopore’s protein based nanopores are the only portable commercial method. Current nanopore based devices have three main issues: Spacial resolution, translocation rate versus sensor strength and dealing with the persistence length of ssDNA. This thesis contributes to ongoing research that aims to create a nanochannel with integrated sensor based sequencing device. The project has two main objectives. The first objective is to improve the protocol for fabricating ssDNA/SWCNT hybrid structures and the second objective is to study the translocation of the hybrid structure through a nanochannel. The success of the first objective will be determined by the amount of singularly wrapped hybrid structures, the amount of unwanted structures and the wrapping characteristics of the singularly wrapped hybrid structures. It was discovered that a 1 minute sonication of a mixture of 1mg SWCNTs to 200µL of the ssDNA stock solution will lead to the best results as about 80% of the hybrid structures resulting from this protocol were singular while there were little to no unwanted structures present. The wrapping characteristics of these samples were a pitch of 11.90nm with a standard deviation of 5.00nm and an angle of 59.7◦ with a standard deviation of 0.9◦ for poly-A and a pitch of 11.73nm with a standard deviation of 5.10nm and an angle of 70.6◦ with a standard deviation of 0.64◦ for poly-T. The translocation of the hybrid structure was studied at different voltages for poly-A and poly-T. It was discovered that the for a voltage of 0.1V around 2 hybrid structures were present for every 20µmx20µm while for 0.5V it was 4 and for 1.0V it was 9. Shorter hybrid structures appear to translocate more prevalent than longer ones and when comparing poly-A and poly-T they delivered similar results.

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