Undergraduate Honors Theses

Thesis Defended

Spring 2012

Document Type

Thesis

Department

Chemistry

First Advisor

Dr. Bruce E. eaton

Abstract

A group of RNAs, referred to as Pdases, which mediate the formation of palladium nanoparticles was discovered through a SELEX process. The Pdases contain 5-(4-pyridylmethyl)-uracil residues without which they are incapable of mediating nanoparticle formation. From previous studies, it is clear that the structures of these RNA molecules play a role in substrate and product specificity, but it is unknown what those structures are and how they vary between the RNA aptamers and between modified and unmodified versions of the RNA. This thesis employs the techniques of thermal melting, circular dichroism, and RNase structure mapping to compare the structures of five selected Pdases to each other. From the melting experiments, it is evident that the Pdases have variable structures that are not formed exclusively from Watson Crick interactions. The Pdases also have different melting profiles if unmodified uracil residues are used in place of the modified bases. The sequences, in both modified and unmodified form, produce circular dichroism spectra characteristic of A-form helices. The spectra, however, are very different from each other in terms of amplitude suggesting that the base modifications affect the structure of the RNA. Finally, structure mapping controls have been completed and moving forward, the technique has the capability of providing more structural detail for the Pdases.

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