Year of Publication

2006

Document Type

Dissertation

College

Arts and Sciences

Department

Chemistry

First Advisor

Stephen M. Testa

Abstract

Group I introns belong to a class of large RNAs that catalyze their own excision from precursor RNA through a two-step process called self-splicing reaction. These self-splicing introns have often been converted into ribozymes with the ability site specifically cleave RNA molecules. One such ribozyme, derived from a self-splicing Pneumocystis carinii group I intron, has subsequently been shown to sequence specifically excise a segment from an exogenous RNA transcript through trans excision-splicing reaction.The trans excision-splicing reaction requires that the substrate be cleaved at two positions called the 5' and 3' splice sites. The sequence requirements at these splice sites were studied. All sixteen possible base pair combinations at the 5' splice site and the four possible nucleotides at the 3' splice site were tested for reactivity. It was found that all base pair combinations at the 5' splice site allow the first reaction step and seven out of sixteen combinations allow the second step to occur. Moreover, it was also found that non-Watson-Crick base pairs are important for 5' splice site recognition and suppress cryptic splicing. In contrast to the 5' splice site, 3' splice site absolutely requires a guanosine.The pathway of the trans excision-splicing reaction is poorly understood. Therefore, as an initial approach, a kinetic framework for the first step (5' cleavage) was established. The framework revealed that substrate binds at a rate expected for RNA-RNA helix formation. The substrate dissociates with a rate constant (0.9 min-1), similar to that for substrate cleavage (3.9 min-1). Following cleavage, the product dissociation is slower than the cleavage, making this step rate limiting for multiple-turnover reactions. Furthermore, evidence suggests that P10 helix forms after the 5' cleavage step and a conformational change exists between the two reaction steps of trans excision-splicing reaction. Combining the data presented herein and the prior knowledge of RNA catalysis, provide a much more detailed view of the second step of the trans excision-splicing reaction.These studies further characterize trans excision-splicing reaction in vitro and provide an insight into its reaction pathway. In addition, the results describe the limits ofthe trans excision-splicing reaction and suggest how key steps can be targeted for improvement using rational ribozyme design approach.

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