Computational methods for understanding RNA catalysis: a molecular approach

Abstract

Molecular simulation is a powerful technology for providing a detailed picture of a wide range of chemical phenomena. The results of simulation studies are now increasingly used in supplementing experimental studies both as a predictive tool and as a lens through which to interpret results and generate new hypotheses. This dissertation describes several advancements in the development and application of molecular simulation methods to the study of RNA catalysis. Such reactions are representative of a broad class of chemistry associated with important biological functions including storage of genetic information, metabolism, and cell signaling and replication. Furthermore, the existence of naturally occuring RNA sequences that catalyze these reactions has significant implications for the origins of life and the potential design of new RNA based technologies. The work presented here offers new insights into these problems and contributes to a detailed, molecular understanding of the fundamental chemical principles that are in action.