| Ribonucleic Acid (RNA) functions as an active component in many biological processes rather than simply being a genetic intermediate between DNA and proteins. Within all three domains of life, RNA has been demonstrated to catalyze reactions, bind small molecule ligands, and directly control the expression of genes. Specifically, recent efforts within the fields of ribozymes and small noncoding RNAs such as miRNAs have expanded the known roles of RNA in biology and thereby have provided platforms for investigating the mechanisms by which the polymer functions within the cell. Herein several RNA switches were studied to assess the mechanism of how RNA folds into a functional molecule and how this molecule can react to a ligand or an environmental change that results in the allosteric rearrangment of RNA structure. Specifically, this dissertation provides a detailed discussion of the function of an engineered ribozyme and three naturally occurring RNA elements that change structure in response to biological metabolites. These newly discovered natural elements, termed riboswitches, control a significant fraction of the genes within certain bacteria. This body of work provides the first detailed study of how these important RNA structures control biological processes. |
