ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
Displaying 1 - 10 of 70
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 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
Description
The ribosome is a ribozyme and central to the biosynthesis of proteins in all organisms. It has a strong bias against non-alpha-L-amino acids, such as alpha-D-amino acids and beta-amino acids. Additionally, the ribosome is only able to incorporate one amino acid in response to one codon. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome enabled the incorporation of both alpha-D-amino acids and beta-amino acids into full length protein. Described in Chapter 2 are five modified ribosomes having modifications in the peptidyltrasnferase center in the 23S rRNA. These modified ribosomes successfully incorporated five different beta-amino acids (2.1 - 2.5) into E. coli dihydrofolate reductase (DHFR). The second project (Chapter 3) focused on the study of the modified ribosomes facilitating the incorporation of the dipeptide glycylphenylalanine (3.25) and fluorescent dipeptidomimetic 3.26 into DHFR. These ribosomes also had modifications in the peptidyltransferase center in the 23S rRNA of the 50S ribosomal subunit. The modified DHFRs having beta-amino acids 2.3 and 2.5, dipeptide glycylphenylalanine (3.25) and dipeptidomimetic 3.26 were successfully characterized by the MALDI-MS analysis of the peptide fragments produced by "in-gel" trypsin digestion of the modified proteins. The fluorescent spectra of the dipeptidomimetic 3.26 and modified DHFR having fluorescent dipeptidomimetic 3.26 were also measured. The type I and II DNA topoisomerases have been firmly established as effective molecular targets for many antitumor drugs. A "classical" topoisomerase I or II poison acts by misaligning the free hydroxyl group of the sugar moiety of DNA and preventing the reverse transesterfication reaction to religate DNA. There have been only two classes of compounds, saintopin and topopyrones, reported as dual topoisomerase I and II poisons. Chapter 4 describes the synthesis and biological evaluation of topopyrones. Compound 4.10, employed at 20 µM, was as efficient as 0.5 uM camptothecin, a potent topoisomerase I poison, in stabilizing the covalent binary complex (~30%). When compared with a known topoisomerase II poison, etoposide (at 0.5 uM), topopyorone 4.10 produced similar levels of stabilized DNA-enzyme binary complex (~34%) at 5 uM concentration.
ContributorsMaini, Rumit (Author) / Hecht, Sidney M. (Thesis advisor) / Gould, Ian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.
ContributorsNangreave, Ryan Christopher (Author) / Hecht, Sidney M. (Thesis advisor) / Yan, Hao (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2013
Description
The effect of earthquake-induced liquefaction on the local void ratio distribution of cohesionless soil is evaluated using x-ray computed tomography (CT) and an advanced image processing software package. Intact, relatively undisturbed specimens of cohesionless soil were recovered before and after liquefaction by freezing and coring soil deposits created by pluviation and by sedimentation through water. Pluviated soil deposits were liquefied in the small geotechnical centrifuge at the University of California at Davis shared-use National Science Foundation (NSF)-supported Network for Earthquake Engineering Simulation (NEES) facility. A soil deposit created by sedimentation through water was liquefied on a small shake table in the Arizona State University geotechnical laboratory. Initial centrifuge tests employed Ottawa 20-30 sand but this material proved to be too coarse to liquefy in the centrifuge. Therefore, subsequent centrifuge tests employed Ottawa F60 sand. The shake table test employed Ottawa 20-30 sand. Recovered cores were stabilized by impregnation with optical grade epoxy and sent to the University of Texas at Austin NSF-supported facility at the University of Texas at Austin for high-resolution CT scanning of geologic media. The local void ratio distribution of a CT-scanned core of Ottawa 20-30 sand evaluated using Avizo® Fire, a commercially available advanced program for image analysis, was compared to the local void ratio distribution established on the same core by analysis of optical images to demonstrate that analysis of the CT scans gave similar results to optical methods. CT scans were subsequently conducted on liquefied and not-liquefied specimens of Ottawa 20-30 sand and Ottawa F60 sand. The resolution of F60 specimens was inadequate to establish the local void ratio distribution. Results of the analysis of the Ottawa 20-30 specimens recovered from the model built for the shake table test showed that liquefaction can substantially influence the variability in local void ratio, increasing the degree of non-homogeneity in the specimen.
ContributorsGutierrez, Angel (Author) / Kavazanjian, Edward (Thesis advisor) / Houston, Sandra (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Heating of asphalt during production and construction causes the volatilization and oxidation of binders used in mixes. Volatilization and oxidation causes degradation of asphalt pavements by increasing the stiffness of the binders, increasing susceptibility to cracking and negatively affecting the functional and structural performance of the pavements. Degradation of asphalt binders by volatilization and oxidation due to high production temperature occur during early stages of pavement life and are known as Short Term Aging (STA). Elevated temperatures and increased exposure time to elevated temperatures causes increased STA of asphalt. The objective of this research was to investigate how elevated mixing temperatures and exposure time to elevated temperatures affect aging and stiffening of binders, thus influencing properties of the asphalt mixtures. The study was conducted in two stages. The first stage evaluated STA effect of asphalt binders. It involved aging two Performance Graded (PG) virgin asphalt binders, PG 76-16 and PG 64-22 at two different temperatures and durations, then measuring their viscosities. The second stage involved evaluating the effects of elevated STA temperature and time on properties of the asphalt mixtures. It involved STA of asphalt mixtures produced in the laboratory with the PG 64-22 binder at mixing temperatures elevated 25OF above standard practice; STA times at 2 and 4 hours longer than standard practices, and then compacted in a gyratory compactor. Dynamic modulus (E*) and Indirect Tensile Strength (IDT) were measured for the aged mixtures for each temperature and duration to determine the effect of different aging times and temperatures on the stiffness and fatigue properties of the aged asphalt mixtures. The binder test results showed that in all cases, there was increased viscosity. The results showed the highest increase in viscosity resulted from increased aging time. The results also indicated that PG 64-22 was more susceptible to elevated STA temperature and extended time than the PG 76-16 binders. The asphalt mixture test results confirmed the expected outcome that increasing the STA and mixing temperature by 25oF alters the stiffness of mixtures. Significant change in the dynamic modulus mostly occurred at four hour increase in STA time regardless of temperature.
ContributorsLolly, Rubben (Author) / Kaloush, Kamil (Thesis advisor) / Bearup, Wylie (Committee member) / Zapata, Claudia (Committee member) / Mamlouk, Michael (Committee member) / Arizona State University (Publisher)
Created2013
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Unsaturated soil mechanics is becoming a part of geotechnical engineering practice, particularly in applications to moisture sensitive soils such as expansive and collapsible soils and in geoenvironmental applications. The soil water characteristic curve, which describes the amount of water in a soil versus soil suction, is perhaps the most important soil property function for application of unsaturated soil mechanics. The soil water characteristic curve has been used extensively for estimating unsaturated soil properties, and a number of fitting equations for development of soil water characteristic curves from laboratory data have been proposed by researchers. Although not always mentioned, the underlying assumption of soil water characteristic curve fitting equations is that the soil is sufficiently stiff so that there is no change in total volume of the soil while measuring the soil water characteristic curve in the laboratory, and researchers rarely take volume change of soils into account when generating or using the soil water characteristic curve. Further, there has been little attention to the applied net normal stress during laboratory soil water characteristic curve measurement, and often zero to only token net normal stress is applied. The applied net normal stress also affects the volume change of the specimen during soil suction change. When a soil changes volume in response to suction change, failure to consider the volume change of the soil leads to errors in the estimated air-entry value and the slope of the soil water characteristic curve between the air-entry value and the residual moisture state. Inaccuracies in the soil water characteristic curve may lead to inaccuracies in estimated soil property functions such as unsaturated hydraulic conductivity. A number of researchers have recently recognized the importance of considering soil volume change in soil water characteristic curves. The study of correct methods of soil water characteristic curve measurement and determination considering soil volume change, and impacts on the unsaturated hydraulic conductivity function was of the primary focus of this study. Emphasis was placed upon study of the effect of volume change consideration on soil water characteristic curves, for expansive clays and other high volume change soils. The research involved extensive literature review and laboratory soil water characteristic curve testing on expansive soils. The effect of the initial state of the specimen (i.e. slurry versus compacted) on soil water characteristic curves, with regard to volume change effects, and effect of net normal stress on volume change for determination of these curves, was studied for expansive clays. Hysteresis effects were included in laboratory measurements of soil water characteristic curves as both wetting and drying paths were used. Impacts of soil water characteristic curve volume change considerations on fluid flow computations and associated suction-change induced soil deformations were studied through numerical simulations. The study includes both coupled and uncoupled flow and stress-deformation analyses, demonstrating that the impact of volume change consideration on the soil water characteristic curve and the estimated unsaturated hydraulic conductivity function can be quite substantial for high volume change soils.
ContributorsBani Hashem, Elham (Author) / Houston, Sandra L. (Thesis advisor) / Kavazanjian, Edward (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
Description
The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation.
ContributorsMartin, James (Author) / Frasch, Wayne D (Thesis advisor) / Chandler, Douglas (Committee member) / Gaxiola, Roberto (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2012
Description
This thesis presents a probabilistic evaluation of multiple laterally loaded drilled pier foundation design approaches using extensive data from a geotechnical investigation for a high voltage electric transmission line. A series of Monte Carlo simulations provide insight about the computed level of reliability considering site standard penetration test blow count value variability alone (i.e., assuming all other aspects of the design problem do not contribute error or bias). Evaluated methods include Eurocode 7 Geotechnical Design procedures, the Federal Highway Administration drilled shaft LRFD design method, the Electric Power Research Institute transmission foundation design procedure and a site specific variability based approach previously suggested by the author of this thesis and others. The analysis method is defined by three phases: a) Evaluate the spatial variability of an existing subsurface database. b) Derive theoretical foundation designs from the database in accordance with the various design methods identified. c) Conduct Monti Carlo Simulations to compute the reliability of the theoretical foundation designs. Over several decades, reliability-based foundation design (RBD) methods have been developed and implemented to varying degrees for buildings, bridges, electric systems and other structures. In recent years, an effort has been made by researchers, professional societies and other standard-developing organizations to publish design guidelines, manuals and standards concerning RBD for foundations. Most of these approaches rely on statistical methods for quantifying load and resistance probability distribution functions with defined reliability levels. However, each varies with regard to the influence of site-specific variability on resistance. An examination of the influence of site-specific variability is required to provide direction for incorporating the concept into practical RBD design methods. Recent surveys of transmission line engineers by the Electric Power Research Institute (EPRI) demonstrate RBD methods for the design of transmission line foundations have not been widely adopted. In the absence of a unifying design document with established reliability goals, transmission line foundations have historically performed very well, with relatively few failures. However, such a track record with no set reliability goals suggests, at least in some cases, a financial premium has likely been paid.
ContributorsHeim, Zackary (Author) / Houston, Sandra (Thesis advisor) / Witczak, Matthew (Committee member) / Kavazanjian, Edward (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2014