Engineering Molecular Probes for Diagnostic Applications

Abstract

Abstract In the wake of the SARS-CoV-2 pandemic, the need for rapid and highly sensitive pathogen testing became apparent. The use of lateral flow and PCR-based assays were limited by sensitivity and time, respectively. Biosensors with an electronic transduction element provide a way to address the needs of rapid detection arising from the pandemic and can be applied to various industries and fields of biomedical sciences. In this thesis, I address some of the key limitations in detecting SARS-CoV-2 using field effect transistor technology, while exploring key conditions to enhance biomolecular detection and build a platform for multiplexed detection of target analytes in a highly sensitive fashion. Through collaboration with investigators at the NYU Tandon School of Engineering, we designed and fabricated a graphene field effect transistor (GFET) platform for broad pathogen detection and demonstrate its ability to detect live SARS-CoV-2 viral particles, as well as spike protein. By implementing thermochemical scanning probe lithography, we conjugated multiple probe types and tested their performance, including antibodies, aptamers and peptides. Through systematic testing, we evaluated the probe length and ionic strength of the testing matrix as key determinants of the theoretical sensitivity, as they affect a critical factor: the Debye length (detection distance from the surface of the FET). In addition to viral detection, we engineered a novel probe for bacterial detection, which exploits the ability of bacteria to cleave specific DNA sequences using highly conserved enzymes (restriction endonucleases). For proof of concept, we tested our probe using a commonly exploited restriction enzyme, EcoRI, and demonstrate viability with a clinically relevant, pathogenic strain of Neisseria gonorrhea. These DNA-based probes exhibit regenerative capabilities and are highly customizable to different pathogens and detection modalities. Together, this work highlights progress in the effort for increased efficiency in pathogen detection using biosensors; both structurally and through designing a new class of molecular probes.