Novel Biosensors for Early Cancer Detection: Development of gold nanoparticle and CRISPR-Cas assays for the optical detection of cancer biomarkers in urine

The earliest form of medical diagnosis is the practice of uroscopy. Although uroscopy is no longer as prevalent in modern medicine as it used to be, multiple diseases can still be diagnosed in urine. This thesis presents optical techniques for early cancer detection in urine. However, instead of looking at the color or assessing the taste of the urine, the focus is on the biomarkers present in the urine. Biomarkers are biomolecules that, at certain levels, can indicate whether people are ill, what type of disease they suffer from, and what the stage of the disease is. The biomolecule we are interested in is deoxyribonucleic acid (DNA), more specifically, the methylated cytosine within the DNA. While cytosine methylation is a healthy process, methylation of promoter CpG islands has also been shown to be a critical hallmark in many cancer cells. This is because specific genes on the DNA must always be expressed to prevent a "normal" cell from becoming a cancer cell. Thus, if we detect cytosine methylation of these specific "cancer regulatory" pieces of DNA (on the promoter CpG islands of these genes), we can say with great certainty that these pieces originate from a cell that is either a cancer cell or a cell that is in the process of becoming a cancer cell. In this thesis, two different approaches are presented for detecting this CpG methylation on specific genes. Part I, entitled "Plasmonic Detection," covers gold nanoparticle-based techniques for (digital) DNA molecule detection. Part II is entitled "CRISPR/Cas Diagnostics" and covers the use of the Cas12a protein for the detection of hypermethylation in specific DNA sequences.