First Advisor

Niles Lehman

Date of Publication

Spring 5-10-2016

Document Type

Dissertation

Degree Name

Doctor of Philosophy (Ph.D.) in Chemistry

Department

Chemistry

Language

English

Subjects

RNA, Genetic recombination, Game theory, Molecular evolution

DOI

10.15760/etd.2915

Physical Description

1 online resource (ix, 150 pages)

Abstract

How life originated from physical and chemical processes is one of the great questions still unanswered today. Studies towards this effort have transitioned from the notion of a single self-replicating entity to the idea that a network of interacting molecules made this initial biological leap. In order to understand the chemical kinetic and thermodynamic mechanisms that could engender pre-life type networks we present an empirical characterization of a network of RNA recombinase molecules. We begin with 1-, 2-, and 3-molecular ensembles and provide a game theoretic analysis to describe the frequency dependent dynamics of competing and cooperating RNA genotypes. This is then extended to 4- and 5-membered networks where varying topologies are compared and mechanisms that could lead to preferential growth and selection of genotypes are described. At the core of these network connections is ribozyme catalysis initiated through a 3-nucleotide base-pairing interface. With the development of a fluorescence anisotropy method, we are able to illustrate a correlation between these binding thermodynamics and network outcomes. Finally, we consider how the heterogeneity of the environment could impact network dynamics and develop a spectrum of spatial inducing methods in which our chemical populations can be probed. These experiments illustrate simple chemical dynamics of RNA interactions, yet these very processes are the foundation for building complexity and ultimately from where selection and evolvability derive.

Rights

In Copyright. URI: http://rightsstatements.org/vocab/InC/1.0/ This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).

Persistent Identifier

http://archives.pdx.edu/ds/psu/17481

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