Exploring Raman spectroscopy for developing prototypes in nanopore DNA sequencing

• Main Author: See, Josephine Si Yu
• Other Authors: Gao Weibo
• Format: Final Year Project
• Language: English
• Published: Nanyang Technological University 2024
• Subjects: Physics; Raman spectroscopy; Nanopore DNA sequencing
• Online Access: https://hdl.handle.net/10356/175720
• Institution: Nanyang Technological University

Nanopore DNA sequencing is transforming genomics with its rapid processing of long DNA strands, providing quick results without the need for DNA amplification or labelling. It offers the distinct advantage of sequencing longer DNA fragments, aiding in complex genome assembly and the identification of structural variations. Its portability allows for on-site genomic studies and immediate diagnostics, even in the most remote areas. The cost-effectiveness of nanopore sequencing is increasing its accessibility for a variety of research and clinical applications. Real-time analysis capabilities are critical for prompt data interpretation, especially during urgent situations like disease outbreaks. This technology's ability to directly read DNA molecules reduces the potential for errors associated with sample preparation. Furthermore, it eliminates the requirement for DNA fragmentation, thus maintaining the genome's integrity. Nanopore sequencing's single-molecule approach provides a detailed look into genetic diversity, and it can also detect epigenetic modifications such as DNA methylation in real-time. These benefits mark nanopore DNA sequencing as a vital tool for the advancement of personalized medicine and genomic research. This paper explores the different fabrication steps to make a device prototype, and performs Raman spectroscopy for developing suitable size prototypes in nanopore DNA sequencing. In recent spectroscopic experiments, the application of a 785 nm line laser yielded distinct Raman peaks at positions characteristic of thymine, while a 633 nm point laser produced peaks corresponding to guanine signatures. This discrepancy raises questions about the underlying complexities, such as phase shifts, that may affect the outcomes, considering the DNA in question was thymine. Further examination revealed that dimer structures with widths of 100 nm and varying lengths between 30 nm and 140 nm were conducive to enhanced Raman signal detection. Moving forward, the focus will be on the fabrication and rigorous testing of these promising dimer designs, to refine the accuracy of nucleotide identification using Raman spectroscopy.