Year of Publication

2005

Document Type

Dissertation

College

Arts and Sciences

Department

Chemistry

First Advisor

Stephen M. Testa

Abstract

Group I introns are catalytic RNAs capable of self-splicing out of RNA transcripts. Ribozymes derived from these group I introns are used to explore the molecular recognition properties involved in intron catalysis. New ribozyme reactions are designed based on the inherent ability of these ribozymes to perform site-specific nucleophilic attacks. This study explores the molecular recognition properties of group I intron-derived ribozyme reactions and describe a new ribozyme reaction involving molecular recognition properties previously not seen.We report the development, analysis, and use of a new combinatorial approach to analyze the substrate sequence dependence of suicide inhibition, cyclization, and reverse cyclization reactions catalyzed by a group I intron from the opportunistic pathogen Pneumocystis carinii. We demonstrate that the sequence specificity of these Internal Guide Sequence (IGS) mediated reactions is not high, suggesting that RNA targeting strategies which exploit tertiary interactions could have low specificity due to the tolerance of mismatched base pairs.A group I intron-derived ribozyme from P. carinii has been previously shown to bind an exogenous RNA substrate, splice-out an internal segment, and then ligate the two ends back together (the trans excision-splicing reaction). We now report that a group I intron derived ribozyme from the ciliate Tetrahymena thermophila can also perform the trans excision-splicing reaction, although not nearly as well as the P. carinii ribozyme.In addition, we discovered a new ribozyme reaction called trans insertion-splicing where the P. carinii ribozyme binds two exogenous RNA substrates and inserts one directly into the other. Although this reaction gives the reverse products of the trans excision-splicing reaction, the trans insertion-splicing reaction is not simply the reverse reaction. The ribozyme recognizes two exogenous substrates through more complex molecular recognition interactions than what has been previously seen in group I intron-derived ribozyme reactions. We give evidence for this new reaction mechanism composed of three steps, with intermediates attached to the ribozyme.

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