Thesis advisor: Abhisheck Chatterjee / The genetic codon expansion (GCE) is a technique that uses an orthogonal tRNA/aminoacyl-tRNA synthetase (aaRS) pair to incorporate noncanonical amino acids (ncAA) into proteins, to enable more protein-based chemistry. In the past two decades, more than 200 ncAAs have been site-specifically introduced into proteins in E. coli, and facilitated studies of protein structures, functions and interaction with other molecules. Although a large variety of ncAAs are available for incorporation in the bacterial systems, significantly fewer ncAAs are accessible for incorporation in eukaryotic cells. An expanded GCE toolbox will be beneficial for numerous applications in eukaryotic systems. Currently, introducing ncAAs in eukaryotes predominantly relies on the archaeal pyrrolysyl tRNA/aaRS pair. Such a strong dependence on a single platform has precluded genetic encoding of many desirable ncAAs, including structural mimics of many important post-translational modifications. The work presented in this thesis first developed an engineered E. coli leucyl tRNA/aaRS pair to enable site-specific incorporation of citrulline, an important PTM, into proteins expressed in mammalian cells. This technology was used to reveal the role of citrullination on site R372 and R374 of PAD4. Additionally, aiming at genetically encoding more diverse ncAAs, all 20 E. coli derived tRNA/aaRS pairs were screened for their ability to suppress TAG and TGA in mammalian cells. This study revealed several tRNA/aaRS pairs that are suitable for ncAA incorporation in mammalian cells, including those selective for phenylalanine, lysine, arginine, serine and glutamine. Efforts are currently under way to engineer these pairs to genetically encode new structural classes of ncAAs. / Thesis (PhD) — Boston College, 2022. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.