Matching Items (3)
Filtering by

Clear all filters

151693-Thumbnail Image.png
Description
The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules

The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.
ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
153134-Thumbnail Image.png
Description
This dissertation shows that the central conceptual feature and explanatory motivation of theories of evolutionary directionality between 1890 and 1926 was as follows: morphological variation in the developing organism limits the possible outcomes of evolution in definite directions. Put broadly, these theories maintained a conceptual connection between development and evolution

This dissertation shows that the central conceptual feature and explanatory motivation of theories of evolutionary directionality between 1890 and 1926 was as follows: morphological variation in the developing organism limits the possible outcomes of evolution in definite directions. Put broadly, these theories maintained a conceptual connection between development and evolution as inextricably associated phenomena. This project develops three case studies. The first addresses the Swiss-German zoologist Theodor Eimer's book Organic Evolution (1890), which sought to undermine the work of noted evolutionist August Weismann. Second, the American paleontologist Edward Drinker Cope's Primary Factors (1896) developed a sophisticated system of inheritance that included the material of heredity and the energy needed to induce and modify ontogenetic phenomena. Third, the Russian biogeographer Leo Berg's Nomogenesis (1926) argued that the biological world is deeply structured in a way that prevents changes to morphology taking place in more than one or a few directions. These authors based their ideas on extensive empirical evidence of long-term evolutionary trajectories. They also sought to synthesize knowledge from a wide range of studies and proposed causes of evolution and development within a unified causal framework based on laws of evolution. While being mindful of the variation between these three theories, this project advances "Definitely Directed Evolution" as a term to designate these shared features. The conceptual coherence and reception of these theories shows that Definitely Directed Evolution from 1890 to 1926 is an important piece in reconstructing the wider history of theories of evolutionary directionality.
ContributorsUlett, Mark Andrew (Author) / Laubichler, Manfred D (Thesis advisor) / Hall, Brian K (Committee member) / Lynch, John (Committee member) / Maienschein, Jane (Committee member) / Smocovitis, Vassiliki B (Committee member) / Arizona State University (Publisher)
Created2014
150268-Thumbnail Image.png
Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors

A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011