Date of Graduation

7-2026

Document Type

Thesis

Degree Name

Master of Science in Biomedical Engineering (MSBME)

Degree Level

Graduate

Department

Biomedical Engineering

Advisor/Mentor

Tung, Steve

Committee Member

Balachandran, Kartik

Second Committee Member

Harris, Leonard

Keywords

DNA sequencing; embossing; fabrication; microchannel; nano embossing; nanochannel

Abstract

DNA sequencing has become increasingly important in the field of biomedical research and clinical applications. Currently, the most well-established sequencing technique is ‘Sequencing by Synthesis’ with accuracy in the range of 99.2% to 99.74% and sequencing lengths of only 300 base pairs. Sequencing by Synthesis is a lab-based method that requires expensive equipment and fast parallel computing. It is not suitable for portable, on-site applications. A new technique known as ‘nanopore’ was developed to meet these requirements. Nanopore is an electrical sequencing method that relies on the translocation of a DNA molecule through a nanoscale pore, where the blockage current is used to identify the sequence. Commercial nanopores are fabricated from proteins and have a shelf life of only 3 months. Recent efforts have focused on developing a synthetic option. One of the promising techniques is a nanochannel-based system integrated with nanoscale DNA sequencing sensors. The primary goal of this design is to provide a portable and cost-effective method for sequencing that does not expire. Additionally, the portability and affordability of this design strike at the weaknesses of ‘Sequencing by Synthesis’. The primary objective of this thesis is to design, fabricate, and test a Polydimethylsiloxane (PDMS) based nanochannel using nano-embossing. Work was performed to establish a fabrication process flow that delivers consistent and robust nanochannels. A step-by-step fabrication protocol was developed, and the nanochannels were fluid tested to assess flow capabilities. Key accomplishments of the present work include a unique nanochannel design, a novel embossing technique to fabricate nanochannels, a strong substrate-to-PDMS bonding technique, and a steady flow of fluid through the nanochannels. Atomic force microscopy and scanning electron microscopy were used together to determine the dimensions of the nanochannels and their connectivity to the microchannels. These images, along with the fluid testing results, demonstrate a repeatable and cost-effective way to fabricate nanochannels for use in a portable DNA sequencing system. Nanochannels fabricated this way are also ready to be integrated with micro- and nanofluidic systems designed for other biological and biomedical applications.

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