Biology Guest Seminar Series - Dr. Thorsten Dieckmann

Speaker:  Dr. Thorsten Dieckmann
(Associate Professor, Dept. of Chemistry, University of Waterloo)
Title of Seminar:  "Catalysis in an RNA World"

Host:  Dr. J.D. Spafford
All are welcome!

Abstract:  The role of RNA as a catalyst in living cells is today well established with numerous examples ranging from protein synthesis in the ribosome to post-transcriptional processing in viruses and possibly the splicesosome. The discovery of this key biological function, which was previously a domain reserved to protein enzymes, in a nucleic acid was initially very surprising because of the perceived lack of chemical diversity in RNA . Even today, after more than 20 years, many questions regarding the mechanisms by which RNA achieves its remarkable catalytic potential and the origin of chemical catalysis in RNA are a focus of intense research. Over the past decade the range of chemistry that is accessible to RNA based catalysis has been greatly expanded beyond the examples found in nature. In vitro selection and evolution based studies have produced novel ribozymes that can achieve significant rate enhancements in chemical reactions as diverse as Diels-Alder additions and RNA alkylation. These new examples of RNA based catalysis lend support to the concept of an RNA world in which RNA served as the primary catalyst and information carrier of the first living cells. We have shown previously, that ligands can undergo significant changes in their electronic structure and charge distribution when bound inside an RNA binding pocket. In this case the malachite green molecule responds to the unique electrostatic environment inside the RNA aptamer with a redistribution of its positive charge as well as a conformational change. These observations suggested that environment inside the RNA binding pocket can have a significant effect on the chemical properties of the bound ligand and lead us to investigate the possibility that the RNA aptamer can be converted into a primitive ribozyme when presented with a suitable substrate molecule. Further studies revealed that the malachite green aptamer can indeed act as a ribozyme. An acetyl-ester derivative of malachite green undergoes an accelerated hydrolysis reaction when bound to the aptamer. Within the RNA binding pocket the reaction proceeds about 10 times faster than background reaction in the absence of RNA. This seems like a very minimal rate enhancement, however, the RNA catalyzed hydrolysis proceeds via a proton driven mechanism rather than the standard hydroxyl driven pathway. If the rate enhancement is compared on a "by mechanism" basis, the RNA achieves an approximately 1000-fold rate enhancement of the proton driven reaction pathway. This is a respectable accomplishment for a molecule that was never subjected to any evolutionary or selective pressure with respect to catalytic potential. Furthermore, this rate enhancement is largely due to electrostatic transition state stabilization. This intrinsic catalytic potential of the aptamer suggests that the molecule might be capable of catalyzing other reactions that can take advantage of the unique electrostatic environment within the RNA binding pocket.