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- Genre: Doctoral Dissertation
- Genre: Masters Thesis
- Creators: Yu, Hongbin
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
Fluxgate sensors are magnetic field sensors that can measure DC and low frequency AC magnetic fields. They can measure much lower magnetic fields than other magnetic sensors like Hall effect sensors, magnetoresistive sensors etc. They also have high linearity, high sensitivity and low noise. The major application of fluxgate sensors is in magnetometers for the measurement of earth's magnetic field. Magnetometers are used in navigation systems and electronic compasses. Fluxgate sensors can also be used to measure high DC currents. Integrated micro-fluxgate sensors have been developed in recent years. These sensors have much lower power consumption and area compared to their PCB counterparts. The output voltage of micro-fluxgate sensors is very low which makes the analog front end more complex and results in an increase in power consumption of the system. In this thesis a new analog front-end circuit for micro-fluxgate sensors is developed. This analog front-end circuit uses charge pump based excitation circuit and phase delay based read-out chain. With these two features the power consumption of analog front-end is reduced. The output is digital and it is immune to amplitude noise at the output of the sensor. Digital output is produced without using an ADC. A SPICE model of micro-fluxgate sensor is used to verify the operation of the analog front-end and the simulation results show very good linearity.
ContributorsPappu, Karthik (Author) / Bakkaloglu, Bertan (Thesis advisor) / Christen, Jennifer Blain (Committee member) / Yu, Hongbin (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
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
Integrated photonics requires high gain optical materials in the telecom wavelength range for optical amplifiers and coherent light sources. Erbium (Er) containing materials are ideal candidates due to the 1.5 μm emission from Er3+ ions. However, the Er density in typical Er-doped materials is less than 1 x 1020 cm-3, thus limiting the maximum optical gain to a few dB/cm, too small to be useful for integrated photonics applications. Er compounds could potentially solve this problem since they contain much higher Er density. So far the existing Er compounds suffer from short lifetime and strong upconversion effects, mainly due to poor quality of crystals produced by various methods of thin film growth and deposition. This dissertation explores a new Er compound: erbium chloride silicate (ECS, Er3(SiO4)2Cl ) in the nanowire form, which facilitates the growth of high quality single crystals. Growth methods for such single crystal ECS nanowires have been established. Various structural and optical characterizations have been carried out. The high crystal quality of ECS material leads to a long lifetime of the first excited state of Er3+ ions up to 1 ms at Er density higher than 1022 cm-3. This Er lifetime-density product was found to be the largest among all Er containing materials. A unique integrating sphere method was developed to measure the absorption cross section of ECS nanowires from 440 to 1580 nm. Pump-probe experiments demonstrated a 644 dB/cm signal enhancement from a single ECS wire. It was estimated that such large signal enhancement can overcome the absorption to result in a net material gain, but not sufficient to compensate waveguide propagation loss. In order to suppress the upconversion process in ECS, Ytterbium (Yb) and Yttrium (Y) ions are introduced as substituent ions of Er in the ECS crystal structure to reduce Er density. While the addition of Yb ions only partially succeeded, erbium yttrium chloride silicate (EYCS) with controllable Er density was synthesized successfully. EYCS with 30 at. % Er was found to be the best. It shows the strongest PL emission at 1.5 μm, and thus can be potentially used as a high gain material.
ContributorsYin, Leijun (Author) / Ning, Cun-Zheng (Thesis advisor) / Chamberlin, Ralph (Committee member) / Yu, Hongbin (Committee member) / Menéndez, Jose (Committee member) / Ponce, Fernando (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
This dissertation is on the study of structural and optical properties of some III-V and II-VI compound semiconductors. The first part of this dissertation is a study of the deformation mechanisms associated with nanoindentation and nanoscratching of InP, GaN, and ZnO crystals. The second part is an investigation of some fundamental issues regarding compositional fluctuations and microstructure in GaInNAs and InAlN alloys. In the first part, the microstructure of (001) InP scratched in an atomic force microscope with a small diamond tip has been studied as a function of applied normal force and crystalline direction in order to understand at the nanometer scale the deformation mechanisms in the zinc-blende structure. TEM images show deeper dislocation propagation for scratches along <110> compared to <100>. High strain fields were observed in <100> scratches, indicating hardening due to locking of dislocations gliding on different slip planes. Reverse plastic flow have been observed in <110> scratches in the form of pop-up events that result from recovery of stored elastic strain. In a separate study, nanoindentation-induced plastic deformation has been studied in c-, a-, and m-plane ZnO single crystals and c-plane GaN respectively, to study the deformation mechanism in wurtzite hexagonal structures. TEM results reveal that the prime deformation mechanism is slip on basal planes and in some cases, on pyramidal planes, and strain built up along particular directions. No evidence of phase transformation or cracking was observed in both materials. CL imaging reveals quenching of near band-edge emission by dislocations. In the second part, compositional inhomogeneity in quaternary GaInNAs and ternary InAlN alloys has been studied using TEM. It is shown that exposure to antimony during growth of GaInNAs results in uniform chemical composition in the epilayer, as antimony suppresses the surface mobility of adatoms that otherwise leads to two-dimensional growth and elemental segregation. In a separate study, compositional instability is observed in lattice-matched InAlN films grown on GaN, for growth beyond a certain thickness. Beyond 200 nm of thickness, two sub-layers with different indium content are observed, the top one with lower indium content.
ContributorsHuang, Jingyi (Author) / Ponce, Fernando A. (Thesis advisor) / Carpenter, Ray W (Committee member) / Smith, David J. (Committee member) / Yu, Hongbin (Committee member) / Treacy, Michael Mj (Committee member) / Arizona State University (Publisher)
Created2013
Description
One dimensional (1D) and quasi-one dimensional quantum wires have been a subject of both theoretical and experimental interest since 1990s and before. Phenomena such as the "0.7 structure" in the conductance leave many open questions. In this dissertation, I study the properties and the internal electron states of semiconductor quantum wires with the path integral Monte Carlo (PIMC) method. PIMC is a tool for simulating many-body quantum systems at finite temperature. Its ability to calculate thermodynamic properties and various correlation functions makes it an ideal tool in bridging experiments with theories. A general study of the features interpreted by the Luttinger liquid theory and observed in experiments is first presented, showing the need for new PIMC calculations in this field. I calculate the DC conductance at finite temperature for both noninteracting and interacting electrons. The quantized conductance is identified in PIMC simulations without making the same approximation in the Luttinger model. The low electron density regime is subject to strong interactions, since the kinetic energy decreases faster than the Coulomb interaction at low density. An electron state called the Wigner crystal has been proposed in this regime for quasi-1D wires. By using PIMC, I observe the zig-zag structure of the Wigner crystal. The quantum fluctuations suppress the long range correla- tions, making the order short-ranged. Spin correlations are calculated and used to evaluate the spin coupling strength in a zig-zag state. I also find that as the density increases, electrons undergo a structural phase transition to a dimer state, in which two electrons of opposite spins are coupled across the two rows of the zig-zag. A phase diagram is sketched for a range of densities and transverse confinements. The quantum point contact (QPC) is a typical realization of quantum wires. I study the QPC by explicitly simulating a system of electrons in and around a Timp potential (Timp, 1992). Localization of a single electron in the middle of the channel is observed at 5 K, as the split gate voltage increases. The DC conductance is calculated, which shows the effect of the Coulomb interaction. At 1 K and low electron density, a state similar to the Wigner crystal is found inside the channel.
ContributorsLiu, Jianheng, 1982- (Author) / Shumway, John B (Thesis advisor) / Schmidt, Kevin E (Committee member) / Chen, Tingyong (Committee member) / Yu, Hongbin (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2012
Description
As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.
ContributorsHan, Dongran (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Ros, Anexandra (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012