Part I: Spectroscopic characterization of sol-gel-derived materials and dendritic compounds amenable to optical chemical sensor development. Part II: Steps towards the development of general aminoacylation of transfer RNA molecules via RNA-based cataly

Sol-gel-processed materials, which are made under room temperature conditions, can accommodate a variety of dopant molecules within their silica matrix, including thermally labile chemical and biochemical recognition elements. Moreover, under carefully chosen condition of hydrolysis, condensation, and curing, one can tune the morphology and internal dimensions of the resulting glass or ceramic, making these materials ideally suited for chemical/biochemical sensor applications. Described herein, Part I of this thesis investigates the response of environmentally sensitive fluorescent probes, trapped within the silica ‘cage’ of sol-gel-derived materials, in order to provide both qualitative and quantitative description of the microenvironments present within. Specifically, we use steady state and time-resolved fluorescent techniques to measure the solvent polarity, accessibility, and molecular dynamics surrounding the dopant molecule.; Part II of this thesis provides an introduction into the realm of RNA-based catalysis, and the notion of an RNA world. In addition to being a provocative theory capable of shedding light on primitive life during early earth, the study of RNA catalysis holds great promise as a readily accessible and adaptable catalytic system with a wide range of tunable substrate recognition elements. Using in vitro selection, our laboratory has more recently devised an aminoacyl transfer catalyst, or ribozyme (r24mini), which is capable of charging the 3′ terminus of transfer RNA (tRNA) with an aminoacyl ester moiety. Aminoacyl-tRNA is of critical importance during modern-day translation of proteins and is responsible for the maintenance of fidelity between the genome and corresponding phenotype. However, similarly charged tRNA containing nonnatural or analog amino acids also offer a valuable route in the in vitro synthesis of tailor made proteins. Part II of this thesis describes recent efforts undertaken in our laboratory to perform such aminoacylation on-column, in a multiple turnover catalytic system. Moreover, we show that such on-column aminoacylation facilitates the rapid chromatographic separation and purification of aminoacylated-tRNA. Using a variety of bioconjugative methods, we have since immobilized r24mini to stationary agarose columns, in order to perform on-column aminoacylation and purify the resulting ammoacyl-tRNA. The details of each of these methods, and the corresponding results in percent aminoacylated-tRNA are described within.