RNA mediated assembly of nanostructures

The first chapter of this work presents a comprehensive look at RNA mediated nanoparticle formation. The overall goal of this research is to gain a deeper understanding of the RNA-particle formation mechanism and the basic properties of the materials selected by modified RNA molecules. Understanding such RNA-substrate interactions and how they translate into the physical and chemical characteristics of the nanoparticles they create are important fundamental concepts when considering these biotemplated materials as potential chemical catalysts. The RNA sequences discussed in the first chapter (referred to as Pdases) were discovered using RNA in vitro selection techniques. These Pdases were found to be capable of forming inorganic palladium (Pd) containing nanoparticles with impressive control over an individual particle\u27s size and shape, despite incubation with the same organometallic precursor. This discovery held exciting implications for inorganic nanoparticle design while also generating numerous questions regarding the mechanism of RNA mediated particle growth. The central question that arose after this initial discovery was how could a biomolecule be used to tailor the physical size and shape of inorganic materials? Starting with a chemical proof designed to uncover the composition of the nanoparticles formed by RNA mediation, this chapter investigates the basic material properties of the nanoparticles while also introducing surprising results regarding the effect of multiple sequences on nanoparticle growth outcomes. In the second chapter, the experiments shift to developing methods to investigate nanoparticle growth mechanisms by fluorescence spectroscopy. A fluorescence polarization anisotropy (FPA) assay is presented in which the strengths of the technique are adapted for studying the formation of RNA mediated Pd nanoparticles in real time. This is a unique application of FPA, as it has been adapted to encompass both the biochemical and materials analysis of a single dynamic system. Although the initial studies described in chapter two focus on the growth kinetics of selected Pdases and their organometallic substrate (Pd2DBA3), it is envisioned that this technique can be used to study a variety of biotemplated systems in a similar fashion. For the experiments described, a key interest was to understand if the RNA governed the rates associated with nanoparticle formation and to gain deeper insight in to the potential growth mechanisms of RNA-nanoparticle constructs. Understanding such interactions could help identify the role RNA play in forming materials while also helping to shape the experimental design of future in vitro selections between RNA and materials. The strengths of these FPA experiments are described as well the associated kinetics observed for RNA mediated particle growth. In chapter three, the fundamental concepts surrounding RNA-nanoparticle interactions shifts to the first application-oriented study of RNA mediated nanoparticle formation for chemical catalysis. The product of a second materials selection is presented in which platinum (Pt) rich nanoparticles are formed using pyridyl modified RNA sequences. These RNA-Pt nanoparticle constructs are interfaced with cadmium sulfide (CdS) quantum dots in an effort to assess the ability of the RNA-Pt nanoparticles to serve as functional catalyst for the photocatalytic production of metal hydrides from aqueous solutions at neutral pH. Metal hydride formation is a crucial step in the challenging chemical reaction of water splitting. The results of this hybrid RNA-Pt/CdS water splitting catalyst are described and compared to more traditional catalyst designs. In the final chapter, the combination of concepts and insights gained as presented in chapters 1-3 are systematically combined into the first RNA in vitro selection for photochemically active materials. This novel selection utilizes an RNA library that is chemically modified such that it can both find and assess the ability of a material to perform photon-driven oxidation chemistry in a complex mixture. In order to conduct such a selection, a new DNA phosphoramidite was synthesized and attached to the RNA library prior to beginning the selection. The details of this synthesis are described. Later in this chapter, the results of this complex yet powerful in vitro selection are outlined. In closing, the prospect of using in vitro selection techniques for discovering other chemically active materials is discussed