Nuclear magnetic resonance studies of catalytic RNAs: The Varkud satellite ribozyme.

摘要

It was long believed that RNA had three basic tasks: as a blueprint for protein synthesis (mRNA), as adaptor molecules (tRNA), or as a scaffold for proteins in the ribosome (rRNA). The accidental discoveries of catalytic RNAs in the early 1980's by Cech and Altman shattered this tenet and made way for a paradigm shift in the importance of RNA and its role in evolution. The RNA World theory states that in pre-biotic times before DNA and proteins were present, RNA was responsible for storing genetic information and replication. It sparked enormous interest in the study of RNA's history, present, and future potential as a molecular tool and as anti-cancer and anti-viral therapeutic agents.; One of the most powerful biophysical techniques available to study RNA is nuclear magnetic resonance (NMR). NMR offers the unique combination of being able to simultaneously determine the high-resolution structure and study dynamics of biomolecules. Catalytic RNAs, termed 'ribozymes', offer a unique opportunity to investigate the intimate relationship between structure and function on a molecular level. The primary focus of this study is the VS ribozyme, a naturally occurring RNA sequence that catalyzes self-cleavage and ligation as a part of its replication cycle. Through the study of its tertiary structure, many interesting facets of its catalytic ability were discovered. For example, the secondary structure of this RNA (and perhaps others) is more fluid than once thought. Large-scale conformational changes in the ribozyme before or during catalysis hint at the flexibility of RNA as an enzyme.; Also presented here is a detailed study of the Malachite Green binding aptamer, an RNA molecule selected to specifically bind a series of related, organic dyes. This investigation allowed for the ability to study stacking interactions between an RNA and its ligand in the absence of hydrogen bonding. Finally, the NMR study of a scorpion venom allowed for the identification of a novel class of toxins with interesting toxicology.