UC Irvine

Over the past five decades, there has been a significant increase in the discovery and applications of nucleic acids. Much has expanded since RNA was first postulated to act as an intermediary between DNA and proteins. The rapid discovery of RNAs many roles and functions has allowed researchers to interrogate and uncover new technologies and approaches to not only create therapeutic intervention for multiple disease prognoses, but also expand the repertoire for synthetic and chemical biology pursuits. The inherent complexity of nucleic acids is evolving as more information is uncovered, which in turn allows for the creation of novel approaches to answer fundamental questions. The work presented in this thesis focuses on the discovery, evolution, and development of nucleic acids for multiple applications. First, I discuss the in vitro selection and evolution of synthetic photoriboswitches that bind to a photoactive molecular switch (e.g., amino trans methoxyazobenzene) to act as an optogenetic tool for regulating mRNA translation. Second, I present the development of a novel high-throughput platform that elucidates and demarcates the functional RNA domains from heterogonous in vitro selected populations of aptamers and riboswitches. Third, I discuss the in vitro selection and discovery of human cerebral spinal fluid (CSF) aptamers with the future goal of developing an aptamer-based, point of care detection device. Lastly, I present the development of a ribosome display platform, coined capture the flag, to serve as a translation assay to select for the discovery of translational riboswitches and photoriboswitches.