Physical Sciences and Mathematics Commons^™

Sequential Assembly Of 1-D And 2-D Origami Arrays, Nathan Shin

Theses, Dissertations and Capstones

DNA origami, invented by Paul Rothemund in 2006, provides many possible routes for the synthesis of complex macromolecular assemblies. This project involves the creation of 1-D and 2-D arrays of cross origami to support the development of DNA detection devices by providing precise platforms for these devices. The M13 plasmid is the most commonly used scaffold in DNA nanotechnology, limiting the size and complexity of an individual DNA origami construct. However, by creating larger assemblies, the dimensions can be multiplied. For example, by alternating two different types of cross origami, optical reporters can be separated by 200 nm, which is …

Organizing 6, 5-Carbon Nanotubes On Dna Origami Arrays, Kathryn A. Pitton

Theses, Dissertations and Capstones

Carbon nanotubes¹ are cylindrical carbon molecules and can be considered to be composed of one atom thick sheets of carbon called graphene. They have been at the forefront of nanochemistry due to their strength and multiple properties such as absorption, fluorescence, semiconduction, and light scattering capability. DNA Origami (DO)² has emerged as a novel domain for molecular design, resulting in the generation of numerous one, two, and three-dimensional structures that have provided platforms for the organization of organic species and inorganic nanoparticles through simple modifications. The use of DNA Origami to control the placement of single walled carbon …

Synthesis Of 1,3-Di(4-Pyridinyl)Acetone, Zachary Tyler Boggs

Theses, Dissertations and Capstones

Although isoelectronic to benzene, the reactivity of pyridine-derived compounds can be quite different. Notably, routes to prepare pyridyl analogs to known phenyl compounds can be very different from how the phenyl compounds are made, even when the nitrogen atom would appear to play an insignificant role in the reaction. This is the case for 1,3-di-4-pyridylacetone. Its phenyl analog has been known for over 90 years and is easily prepared, while the only reported synthesis of 1,3-di-4-pyridylacetone occurs in very low yield. We report a preliminary synthesis from common starting materials, albeit in low yield, and offer an explanation for why …

Identifying C-Mannosylatedproteins In Raw264.7 Cells Via In Vitro Hsc70 Co-Immunoprecipitation Strategies, Nicholas Ryan Kegley

Theses, Dissertations and Capstones

C-mannosylation is a specific type of glycosylation in which α-mannose is covalently bound to the C2 atom of a tryptophan via a carbon-carbon bond. Presently, it is known to occur on proteins that contain the W-x-x-W-x-x-W/C motif found within the Thrombospondin Type-1 Repeat (TSR), with ‘x’ denoting any amino acid. C-mannosylation has been implicated in a number of cellular functions, including protein secretion and type I cytokine receptor function. Previous research has shown that exogenous C-mannosylated peptides derived from TSR-containing proteins upregulate the production of the pro-inflammatory cytokine Tumor Necrosis Factor alpha (TNF-α) in RAW264.7 macrophage cells. This upregulation is …

Characterizing The Effects Of Environmental Stressors On The Photosynthetic Capacity Of Chlorella Vulgaris, Amanda Louise Smythers

Theses, Dissertations and Capstones

Chlorella vulgaris is a unicellular green algae grown throughout the world. Due to its multiple trophic modes as well as its ability to maintain high rates of growth under adverse conditions, it has been of global interest for use in ecological contamination studies, biofuel feedstock optimization, and studies of photosynthetic electron transfer. Using a wide-range of methods for physiological and photosynthetic characterization, the studies within seek to further extend the usefulness of C. vulgaris in a variety of environmentally important studies. Once the protocols were optimized specifically for this alga, they could be applied in both ecologically relevant and biodiesel …

Isolation And Identification Of Hsc70 Conjugates In Raw264.7 Murine Macrophage-Like Cells, Michael Arland Parsons

Theses, Dissertations and Capstones

IL12R- β2 is a Type I cytokine receptor and contains the WXXW (WSNWS) sequence that often predicates the post-translational addition of mannose to a tryptophan residue via a carbon-carbon bond. This study will stimulate expression of IL12R- β2 in RAW 264.7 Macrophage-Like Cells by shutting down the extracellular signal kinase (ERK) pathway and introducing inflammatory agents lipopolysaccharide and CpG DNA in order to collect a concentrated sample of IL12R- β2. These samples will be analyzed for the presence of C-mannosyltryptophan residue

Novel Dna Origami Based Lateral Flow Assay Development, Adrienne Walker

Theses, Dissertations and Capstones

Lateral flow assays (LFA) are used for point-of-care qualitative diagnostics of an analyte of interest, often in non-laboratory environments. Traditionally, the format of a lateral flow assay is to utilize immobilized antibodies on a membrane as the capture probe in conjunction with a reporting immunological recognition system for an analyte captured between them in a sandwich format. However, there are several shortcomings of antibodies which recommend their replacement with other recognition elements, if possible. The research described in this thesis was directed toward using several of the inherent properties of DNA based Origami nanostructures to enable the construction of DNA …

Syntheses And Characterization Of [4]Ferrocenophane, Ahmed Sabah Al-Doori

Theses, Dissertations and Capstones

Metallocenophanes are metallocenes in which the cyclopentadienyl ligands are connected by a molecular bridge. Recently, metallocenophanes have received increasing attention because of their structure, chemical reactivity, and potential use as building blocks for new materials. Even though metallocenophanes have been synthesized by different methods, the majority of these methods involved the use of iron with rare examples of other metals. Therefore, a new method was employed that in addition to making ferrocenophane, will allow us to synthesize metallocenophanes with V, Cr, Mn, Co, and Ni as central metals. This thesis reports the synthesis of [4]ferrocenophane via a “flytrap” route. The …

An Investigation Of The Effect Of Mn2+ On The Fth1 Ire-Irp Complex, Eric Thomas Mendenhall

Theses, Dissertations and Capstones

Iron is a widely distributed metal found in almost every physiological system in nature, thus being an essential part of life. Iron homeostasis in the human body must be tightly regulated as iron is both beneficial and harmful to different cellular processes. Ferritin is a protein that has a prominent role in maintaining iron homeostasis via iron sequestration. Additionally, this protein itself is regulated by the Iron Responsive Element (IRE) and its interaction with an apoaconitase protein or the Iron Regulatory Protein (IRP). The binding of the IRP to this IRE, located on the 5’ untranslated stem loop region of …

Glycation Of Lysozyme, Wisam Talib Joudah

Theses, Dissertations and Capstones

For this research project, I propose a method for the analysis of glycated lysozyme using Matrix Associated Laser Desorption / Ionization-Time of Flight Mass spectrometry (MALDI-TOF MS). Glycation or "Maillard reaction" is a non-enzymatic reaction that occurs between amino acid residues, usually primary and secondary amines, of proteins and the carbonyl group of reducing sugars to yield Schiff bases. The glycation mechanism occurs between the carbonyl group of the reducing sugars and a primary amine by nucleophilic addition, resulting in the formation of a Schiff base. The Schiff base can then rearrange into the more stable Amadori product which is …

Investigation Into The Biological Importance And Function Of Proinsulin C-Peptide, Christina L. Newsome

Theses, Dissertations and Capstones

The C-peptide of insulin was thought to be biologically inactive, but recent studies have shown that the C-peptide causes multiple molecular and physiological effects. Evidence has shown that C-peptide binds to a cell surface receptor, probably a G-protein coupled receptor, and that the COOH-terminal pentapeptide is essential for binding and constitutes an active site. For a further understanding of the detailed nature of the physiological effects of C-peptide, the receptor structure needs to be determined. We designed an affinity column using C-peptide to try and gain a better understanding of the biological effects by examining what proteins the affinity column …

Probing A Complex Dissociation Energy Surface With Experimental And Theoretical Methods, Hannah Elizabeth Bott

Theses, Dissertations and Capstones

Dendrimers are hyperbranched polymers with a tree-like structure that can be tuned for size, shape, and functionality. Dendrimers have exhibited numerous possibilities in chemical and biochemical processes as their use in host-guest systems and controlled gene and drug delivery vehicles. Distinct properties of dendrimers, such as well-defined architecture and high ratio of functional moieties to molecular volume, make these polymers substantially useful for the development of nanomaterials and medicines. It has recently been demonstrated that polypropylene-imine (PPI) dendrimers have specific physical properties that are well suited for many applications. More specifically, the nitrile-terminated dendrimer creates a unique environment that is …

Investigation Into The Cellular Actions Of Carnosine And C-Peptide, Emma H. Gardner

Theses, Dissertations and Capstones

Carnosine is a dipeptide composed of beta-alanine and histidine found exclusively in long-lived animal tissues. The cellular action of carnosine is still under extensive investigation; however, it has been proposed to have a role as an anti-oxidant and oxygen free radical scavenger, a physiological buffer, a heavy metal chelator, and has been implicated as an anti-aging agent.^2,4 Our lab has been studying the interaction between carnosine and heme by analyzing both the effect carnosine has on the glycation of the heme containing protein cytochrome c and the interaction of carnosine with free hemin. We have observed that the addition …

The Ph Dependence Of Photosystem Ii Oxygen-Evolving Complex Assembly, Emilee Hope Cook

Theses, Dissertations and Capstones

Photosystem II (PSII) research has gained interest in recent years due to the need for energy production. However the mechanisms of photosystem II photoassembly and water oxidation are not well understood. Therefore the main goal of my research was to understand photoassembly better by determining the pH dependence of oxygen evolving complex (OEC) assembly. These experiments could help to gain a better understanding of D1 (a subunit of photosystem II) degradation and PSII repair as well as determine the amino acid residues involved in the process. However, we had several issues with photoassembly along the way that had to be …

Toward A Comprehensive Model Of Photosystem Ii Oxygen Evolving Complex Photoassembly, James Scott Board Ii

Theses, Dissertations and Capstones

Elucidating the mechanism of photoassembly of the oxygen-evolving complex (OEC) will lead to a better understanding of how nature catalyzes water oxidation. Although the temperature dependence of oxygen evolution has been described in the literature [1,2], we have performed a comprehensive study that covers Photosystem II (PSII) activity oxygen evolution in the presence and absence of 2,6-dichloro-1,4benzoquinone (DCBQ) from 5–45°C. In addition, we performed similar measurements for OEC photoassembly in the absence of DCBQ. PSIIenriched particles used for our measurements were prepared according to Berthold, Babcock, and Yocum[3], with modifications from Kolling, et al.[4] The oxygen-evolution of intact BBY particles …

Interaction Of Pyrimoidiazolium Ions With Calf Thymus Dna, Stormy Rene Gibson

Theses, Dissertations and Capstones

A new class of fluorescent dyes, pyridoimidiazolium cations, is being considered for their possible use in the biochemical field because of their interactions with DNA. Binding of low molecular weight fluorophores has been proven to cause a wide variety of biological responses in DNA. The dyes used here have been synthesized using α-diimine type compounds. The reaction used has the capability to produce many fluorescent cations. Binding constants of these compounds in acetonitrile with calf thymus DNA have been determined by measuring emission intensity. Emission intensity showed the degree to which binding is occurring. The experimental results show that binding …

Synthesis, Characterization And Computational Study Of [4]Octamethylferrocenophane, Benjamin Mark Wilson

Theses, Dissertations and Capstones

This thesis reports the synthesis of an organic molecule, 1,4-bis(2,3,4,5-tetramethylcyclopentadienyl)butane by two different methods, in about 75% and 85% crude yield. Deprotonation of this molecule followed by reaction with FeCl2 generated the tethered ferrocene, [4]octamethylferrocenophane. Although the yield was low in the first attempt (2%), this molecule has been characterized through NMR spectroscopy, X-ray crystallography, electronic spectroscopy, elemental analysis, and decomposition temperature. A computational study was performed to determine the energy gap between each minimum energy structure. It was found that the energy barrier was not high enough to prevent a rapid interconversion between the two structures of minimum energy …

Incorporation Of The Actin-Myosin Biomolecular Motor System Into A Microfluidic Device, Rebecca Marie Ragland

Theses, Dissertations and Capstones

Recently, the field of bionanotechnology has sought to develop a device containing a biomolecular motor nano-cargo transport system. Among many applications, a device of this sort could be used to sort, purify, or detect specific molecules. In this work, an attempt was made to incorporate the actin-myosin biomolecular motor system into a microfluidic device constructed out of polydimethylsiloxane (PDMS) and glass. Methods for cleaning and functionalizing the glass surface of the device were optimized. After performing actin-myosin motility assays in a variety of PDMS/glass devices, it was determined that the oxygen permeability of PDMS limited the quality of motility that …

Utilization Of Dna/Dendron Conjugates For Dna Monolayers On Gold: A Comparative Study, Erik Steven Vint

Theses, Dissertations and Capstones

The uses of single-stranded DNA probes tethered to solid supports have gained interest in recent years due to the increasing number of applications these systems present. However, the traditional methods used to fabricate these monolayers are flawed. The synthesis and purification of multithiol headgroups for improvement upon ssDNA surface attachment for the fabrication of self-assembled monolayers on gold surfaces is described. Generation 4 polyamidoamine dendrons were conjugated to ssDNA oligomers in a one-to-one ratio and functionalized to provide multiple thiol groups for possible surface attachment. Modification of the dendrimer’s amine terminated periphery groups to thiols was confirmed using 1 H …

Elucidation Of Fragmentation Pathways Of Nitrile-Terminated Ppi Dendrimer-Metal Complexes, Kristen Nicole Pack

Theses, Dissertations and Capstones

The complexity of branching macromolecules around a core unit, such as poly(propylene)imine (PPI) dendrimers, has caught the attention of researchers for several years^1,2,3,4,5. The structural framework of the core unit for these dendrimers is simply 1,4- diaminobutane. As the synthesis of higher-order generations of the macromolecule progresses, the molecules become very complex and tightly woven, but have predictable geometries and properties. The PPI dendrimers can be functionalized at the terminal ends of the branches in order to elicit different properties. The PPI dendrimer examined in this project has been terminated with a nitrile group rather than the usual …

Synthesis Of 5-Methoxy-7-Methylbicyclo[3.2.0]Hept-2-En-6-Ol, Harlan Reid

Theses, Dissertations and Capstones

In order to generate a chiral metallocene ligand similar to Kaminsky-Sinn catalysts, a multistep synthesis for the production of 6,7-dimethylbicyclo[3.2.0]hepta-1,3-dienyl anion was proposed. Experiments directed at the initial phase of the proposal are included, ending with the characterization of new alcohols in compounds 9 through 12. Two steps from the synthesis were successfully combined, leading to improved recovery of the alcohols.

High Resolution Single Molecule Optical Localization Of Multiple Fluorophores On Dna Origami Constructs Fluorophores On Dna Origami Constructs, Anuradha Rajulapati

Theses, Dissertations and Capstones

An ongoing challenge in the development of nanoelectronics and nanophotonics is the nondestructive, high-resolution localization in space of single molecules and multi-molecular assemblies. The apparent barrier to the use of optical microscopy at the sub-100 nm scale is the well known Abbe Limit, the diffraction limit to resolution. This laboratory has adapted a technique called Single-molecule high resolution imaging with photobleaching (SHRIMP). We have developed methods for utilizing SHRIMP for the determination of the separation of two fluorophores in single DNA origami constructs.

DNA Origami is extremely useful because it can address nanocomponents down to 2nm separation. It should be …

The Transsulfuration Pathway Significantly Contributes To Glutathione Biosynthesis In Human Mammary Epithelial Cells, Andrea Del Pilar Belalcazar Maya

Theses, Dissertations and Capstones

Cellular methylation and antioxidant metabolism are linked by the transsulfuration pathway, which converts the methionine cycle intermediate homocysteine to cysteine, a precursor for glutathione biosynthesis, principally in hepatic cells. In mammals, the transsulfuration pathway has been identified in liver, kidney, pancreas and brain. To determine whether the pathway exists in mammary cells human breast adenocarcinoma cells (MCF-7) and normal mammary epithelial cells (HMEC) were labeled with ³⁵S-methionine for 24 hours following pre-treatment with a vehicle control, the cysteine biosynthesis inhibitor propargylglycine (PPG) or the gammaglutamyl cysteine synthesis inhibitor buthionine sulfoximine (BSO). Cell lysates were prepared and reacted with glutathione-S-transferase …

Structural Determination Of The 5' Untranslated Regions Of Ire-Containing Mrnas, Chandra Sekhar Bathina

Theses, Dissertations and Capstones

The expression of ferritin and amyloid precursor protein (APP) is post-transcriptionally regulated by iron-regulating proteins via binding to a stem-loop structure known as an iron-responsive element in the 5’-untranslated region (5’UTR) of ferritin and APP mRNAs. In this study, we used atomic force microscopy (AFM) to visualize the conformation of the 5’UTRs of ferritin heavy chain (Ferritin-H), ferritin light chain (Ferritin-L), and APP mRNA transcripts from human and mouse, and determined the secondary RNA structures using selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE). The AFM imaging did not provide high resolution structural information about these RNAs, whereas the SHAPE …

Mass Spectrometry Of Dendrimer Metal Complexes, Jason David Batchelor

Theses, Dissertations and Capstones

Dendrimers are hyper-branched macromolecules with unique properties. They form using a “cascade-like” synthesis involving repetitive reaction steps. These steps are controlled, resulting in monodisperse dendrimers. Synthesis is divergent, core to exterior, or convergent, exterior to core. Dendrimers are created from various molecules with numerous functional properties. They are used as catalysts, diagnostic agents, and others.

This thesis studies 1st generation poly(propylene) imine, consisting of a diaminobutane core with 4 propyl amine branches. Fragmentation of protonated and metal (Co, Ni, Cu and Zn) complexed dendrimers was analyzed by ion-trap mass spectrometry. Two isotopically labeled dendrimers were synthesized for neutral loss identification …

Identification And Analysis Of Prohibitin In B16 Mouse Melanoma Cells, Christopher Francis

Theses, Dissertations and Capstones

Prohibitin, a highly conserved protein found in eukaryotic cells, has been found in recent years to possess a wide variety of functions in the cell. Whereas the mechanisms by which the protein functions are still largely unknown, it is clear that prohibitin possesses very strong anti-proliferative properties in the cell, as well as potentially both nuclear and mitochondrial functions based upon its movement and localization upon apoptotic signaling. Upon treatment with retinoic acid, transformed B16 mouse melanoma cells also indicate a differential expression of prohibitin in which production of the protein is increased. The purpose of this work was to …

Spectroscopic And Thermodynamic Analysis Of Co Rebinding And Photodissociation From Fe (Ii) Lpo, Dustin Michael Lockney

Theses, Dissertations and Capstones

Lactoperoxidase (LPO) is a heme peroxidase found in tears, milk, saliva, and cervical fluids that has bactericidal activity. The bactericidal nature of LPO is due to its ability to oxidize halides and pseudohalides in the presence of H2O2. Full understanding of the catalytic cycle of LPO requires detailed characterization of the mechanism of ligand binding to the enzyme active site. This includes a dynamic and energetic description of conformational changes associated with heme-ligand interactions. Photoacoustic calorimetry is applied to determine the kinetics and magnitude of reaction volume and enthalpy changes for CO dissociation from CO-LPO. Time-resolved absorption spectroscopy was used …

Scanning Probe Microscopy And Oxidation Of Silicon At Breakdown Voltages, Thabo Gcwabaza

Theses, Dissertations and Capstones

The growing importance of Scanning Probe Microscopy (SPM) as a tool for nanofabrication is opening many avenues in lithography nano-science. One type of Scanning Probe Lithography involves electrochemistry at the tip/substrate interface. Atomic Force Microscopy (AFM) with conductive tips and substrates was used in our study to both pattern and image those patterns on silicon substrates. Our long-term objective is to design and fabricate micron-scale patterns of nanometer sized spots on silicon chips that can serve as attachment sites for DNA based nano-arrays. In order to fabricate such substrates a study of the underlying electrochemistry was required. A most promising …

Fluorescence Prediction Through Computational Chemistry, Daniel Craig Lathey

Theses, Dissertations and Capstones

With the growing demand for diverse fluorescent dyes, it is imperative to find a more efficient methodology by which to synthesize dyes. Our research group has found a computational method that can efficiently predict the optical properties of a molecule before it is synthesized. By evaluating different semi-empirical methods, we have found a way to predict the fluorescence maxima. With the new ability of Hyperchem 7.5 to geometrically optimize a molecule in an excited state, we can predict not only the absorption maxima, but we can also predict the fluorescence maxima within 25 nm of the actual fluorescence.

With this …

Temperature And Ph Dependence Of The Cyclization Of Creatine: A Study Via Mass Spectrometry, Brian J. Diamond

Theses, Dissertations and Capstones

The creatine to creatinine cyclization is of significant biological importance, providing energy for muscle cells and indicating proper renal function. From a chemical perspective, the rate at which creatine cyclizes to form creatinine has interested researchers since the late 1920s, but the cyclization is poorly understood both energetically and mechanistically. Mass spectroscopy was used to determine the rate of creatine cyclization as a function of temperature and pH. Using these values, the energetic parameters, activation energy and Arrhenius factor, were determined as a function of pH to better understand this reaction and ultimately determine the mechanistic process for this reaction. …