Physical Sciences and Mathematics Commons^™

Binding Interactions Of Biologically Relevant Molecules Studied Using Surface-Modified And Nanostructured Surfaces, Palak Sondhi

Dissertations

This research focuses on the field of surface nanobioscience, wherein different nanosurfaces that will be used as working electrodes in the electrochemical cell are manufactured and surface modified to understand the critical binding interactions between biologically significant molecules like proteins, carbohydrates, small drug molecules, and glycoproteins. This research is essential if we are to determine whether a synthetic molecule can serve as a therapeutic candidate or diagnose a disease in its early stages. In order to fully understand the binding interactions, the study begins with defining some of the fundamental concepts, principles, and analytical tools for biosensing.

Afterwards, we addressed …

Photophysical Properties Of Synthetic Oligomeric Phenylene Ethynylene, Hugh F. Fritz Jr.

Chemistry and Chemical Biology ETDs

Oligomeric Phenylene Ethynylenes (OPEs) are a class of synthetically prepared compounds with the basic structure of phenylene rings connected by triple-bonded carbon atoms, also known as an ethyne link. This structure can be modified by incorporating functional groups onto one or more of the phenylene rings. The addition of functional groups, such as sulfoxide or imidazole, may alter the photophysical properties in detectable ways. The photophysical techniques used in this report include fluorescence, spectroscopy in the ultraviolet and visible light range (UVVIS), and photon-based excitation using a photo chamber.

One attractive function of OPEs is their antimicrobial property. Previously published …

Structural Integrity And Stability Of Dna In Ionic Liquid And Near-Infrared Indolizine Squaraine Dye, Ember Yeji Suh

Honors Theses

Luminol, the most common presumptive test for blood at a crime scene, has multiple issues, such as false positive results with chemical agents, no luminescence due to “active oxygen” cleaning agents on bloodstains, and inability to penetrate textile materials. A combination of indolizine squaraine dye and ionic liquid (IL), or Dye Enhanced Textile Emission for Crime Tracking (DETECT), have shown potential to address these issues. The purpose of this study was to assess the binding mechanism of CG (1:1) and SO₃SQ dye to HSA and how the mechanism can explain the W214 fluorescence quenching effect and to determine …

Mechanism Of Sila- And Germafluorenes For Biological Applications, Shelby Jarrett

Dissertations

2,7-disubstituted silafluorenes and germafluorenes, originally designed for OLED applications, are a class of fluorescent dyes that have gained recent interest as probes for bioimaging and as biosensors to monitor cellular dynamics and interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Here, their spectral properties are investigated under aqueous conditions for relevant biological applications. These molecules display intense blue fluorescence in the solid state and in solution, have high extinction coefficients, and exhibit appreciable solubility in aqueous solution. To better understand potential applications, the mechanism of fluorescence was investigated. It …

The Design And Testing Of Fluorescence-Based Sensors For Phosphate And Phosphonate, Sara Hassanzadehroknabadi

Electronic Theses and Dissertations

Inorganic phosphate (Pi) is an essential compound for all living things, as it serves as a component of nucleic acids and ATP, which are required for plant growth and proliferation. However, when excess Pi enters the aquatic environment, it has severe detrimental effects through the induction of harmful algal blooms (HAB), which negatively impact aquatic life, the quality of drinking water as well as recreational activities. It is therefore critical to have fast, sensitive, and inexpensive sensors for Pi that quickly and quantitively measure its concentration in a field setting.

Phosphonates or organophosphorus compounds are phosphoric acids possessing alkyl or …

Optimizing The Fluorescent Quantum Yield Of Carbon Dots, Megan B. Prado

MSU Graduate Theses

Carbon dots (CDs) are a subclass of carbon nanomaterials that exhibit unique properties of fluorescence, photostability, low toxicity, and biocompatibility. These unique properties have enabled numerous applications including biosensing, heavy-metal detection, and pH-sensing, among others. Their optical properties can be modified via doping to produce increasingly fluorescent CDs after appropriate purification. Herein, doped CDs were synthesized in four bottom-up methods for comparison using sucrose or citric acid as carbon precursors. Varying hetero-atom dopants (N, S, B) were used in differing molar ratios. The pH-dependent fluorescence and fluorescent quantum yield (QY) were measured for each sample. Characterization was conducted using Fourier-Transform …

Total Internal Reflection: Applications In Nonlinear Microscopy And Fluorescence Anisotropy, Brandon Colon

Doctoral Dissertations

As technology advances to harness new energies and to create new cures, the sophistication of analysis grows not only in depth but in efficiency. Total internal reflection (TIR) has been coupled to microscopy leveraging its unique optical phenomenon on a breadth of topics. In this dissertation, the work presented will show how TIR was applied in two different instrumental analyses to evaluate two unique and complex systems. The first project features TIR paired with the transient absorption microscopy (TAM), a nonlinear optical technique, to gauge solvent mixing and diffusion in microreactors. Microreactors gained acclaim for their ability to produce high …

Instrument Development For High Sensitivity Size Characterization Of Lipid Vesicles And Other Biological Macromolecules Via Taylor Dispersion Analysis, Meagan Moser

Doctoral Dissertations

Just as humans communicate with other humans, the cells in our bodies communicate with each other through various, often complex, mechanisms. Cell-to-cell transmission of small molecules, lipids, proteins, peptides, or nucleic acids can be mediated by extracellular lipid vesicles called exosomes. Exosomes have been found to play a role in the delivery of regulatory molecules from one cell to another, serving as a universal communication mechanism. Currently, there is an emerging focus on characterizing exosome communication dynamics. Understanding exosome mechanisms of cell-to-cell communication requires accurate measurements of the spatiotemporal and chemical dynamics of exosome secretion. No current analytical approach offers …

Preparation And Study Of Bacterial Membrane Models, Enoch Asimbisa

Electronic Theses and Dissertations

Fuel molecules are organic solvents that have disruptive effects on the bacterial membrane. This is a significant barrier in biofuel production, as it limits the fuel concentration that can be achieved through fermentation. One potential way of overcoming this barrier is to identify lipid compositions that can better withstand solvent stress, for which it is important to understand how organic solvents disrupt the membrane. Use of biophysical characterization techniques to quantify physical properties like fluidity and thickness will enable us to understand the mechanism by which solvents disrupt membranes. Native membranes are very complex, and we sought to develop in-vitro …

Synthesis And Characterization Of Re(I) Tricarbonyl Complexes Of 1,8-Naphthalimide, Priyanka Jagadeesa Prabhu

Electronic Thesis and Dissertation Repository

1,8-Naphthalimide fluorophores with amino-substituents absorb and emit in the visible region. The photophysical properties of this class of fluorophores can be modulated by altering the degree of Intramolecular Charge Transfer (ICT) in the excited state. Thus, several metal complexes with the 1,8-naphthalimide motif have been developed as cell imaging agents. In this project, four 1,8-naphthalimide ligands were synthesized by incorporating rigid linkers. Among these, three ligands also allowed the extension of π-conjugation to the naphthalimide moiety. In addition, a ligand was also synthesized without the use of a linker. Re(I) tricarbonyl complexes of these ligands were also synthesized and their …

Part I: Development Of Small-Molecule-Based Probes For The Vitamin D Receptor; Part Ii: Development Of A Scalable Manufacturing Process For Orcein Dye, Tania Roseann Mutchie

Theses and Dissertations

PART I:The vitamin D receptor (VDR) is a ligand-dependent transcription factor and member of the nuclear hormone receptor superfamily. VDR is expressed in the epithelia of endocrine organs, digestive system, bronchi, kidneys, and thymus, as well as being present in leukocytes and bone cells. Cell proliferation, cell differentiation, and immunomodulation, along with calcium and phosphate homeostasis, are all processes regulated by the receptor. Within the cell, VDR can be membrane-bound or located in the nucleus. Nuclear localization of VDR transpires following the binding of vitamin D metabolites, the most active of which is 1α,25-dihydroxyvitamin D3 (calcitriol). Within the nucleus, interactions …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Plasmon Enhanced Single Molecule Fluorescence In Zero Mode Waveguides (Zmws), Abdullah Masud

Theses and Dissertations--Chemistry

Plasmonic nanostructures are an extensive research focus due to their ability to modify the photophysical properties of nearby fluorophores. Surface plasmons (SP), defined as the collective oscillation of delocalized electrons, are the fundamental characteristic primarily responsible for altering those photophysical properties. Studying fluorophores at the single-molecule level has received significant attention since more specific information can be extracted from single molecule-based studies, which otherwise could be obscured in ensemble studies. However, single-molecule studies are inherently challenging because the signal from a single molecule is usually dim, making it difficult to detect. The situation is even worse in a crowded environment …

Effect Of Electron Demand On Sensing Behavior Of Carbazolopyridinophanes, Grace Abban

Theses and Dissertations

Hydrazine (HZ), monomethylhydrazine (MMH), and 1,1-dimethylhydrazine (UDMH) are widely used as high energy rocket propellants in bipropellant rocket engines. However, hydrazine and its derivatives are highly flammable and carcinogenic. Currently, hydrazine sensors used for detection are irreversible which makes them costly. Two proposed carbazolopyridinophanes containing intramolecular hydrogen bonds were synthesized to detect hydrazine as real-time reversible sensors. However, their thresholds for detection (100 and 25 ppb for CPand 22OMeCPrespectively) were above the regulatory limit of 10 ppbdue to background fluorescence. It was established that the quenching of carbazole in the presence of the CP system has a direct correlation to …

Novel Substrate-Free Cholinesterase Based Sensing Of Organophosphorus Compounds, Hailey J. Marini

Legacy Theses & Dissertations (2009 - 2024)

The increasing concerns of chemical weapons used by terrorists is growing, creating a need for infield detection methods that can rapidly detect these compounds that are a major health concern for civilians and military personnel. Displacement is a novel concept for the detection of cholinesterase inhibitors, including organophosphorus compounds, that could replace the classical instrumentation methods currently being used for diagnostics.

Towards Machine Learning In Chemical Sensing : Milk Differentiation And Quality Control Through Two-Dimensional Nano-Sensor Array, Yu Sheng Chen

Legacy Theses & Dissertations (2009 - 2024)

Herein, we developed a novel artificial tongue using machine learning and 12 nanoassemblies (2D-NAs) to identify and analyzed different kinds of milk beverages for quality control. This biomimetic sensor array was trained to “taste” different milk types as an “artificial tongue” which is the first time we demonstrated that this sensor array can be implemented to complex systems. Two-dimensional nanoparticles (2D-nps) and nine fluorescently labeled single stranded oligonucleotides (ssDNA) with different length and nucleobases were assembled to create 12 2D-NAs. The artificial tongue was deployed to identify and analyze five milk types. All five milk types were discriminated with 95% …

Optimal Excitation Wavelength For Raman Spectroscopic Analysis Of Organic Gunshot Residue Evidence, Ashley Hull

Legacy Theses & Dissertations (2009 - 2024)

Gunshot residue (GSR) is a type of trace evidence that can often be recovered at violent crime scenes. There are two major types of GSR, organic gunshot residue (OGSR), and inorganic gunshot residue (IGSR). Traditional forensic analysis of GSR focuses on IGSR, although with the movement towards lead-free, or non-toxic ammunition, IGSR analysis has become less informative, as lead is a major component of IGSR analysis. Because of this, OGSR has been investigated to supplement the standard IGSR analysis methods. Previous work has shown Raman spectroscopy to be effective at identifying OGSR as well as a minimally destructive and specific …

Smart Sensors With Dual Modes Of Signal Transduction For Monitoring Molecules Pertinent To Health And The Environment, Jared T. Wabeke

Dissertations

The dissertation focuses on the design and synthesis of smart materials for the detection of molecules pertinent to environmental protection and healthcare. The use of computational simulations is pivotal toward advancing molecular design for targeted applications. Research was conducted to investigate the use of simulations to develop novel sensors with dual modes of signal transduction. The molecular properties were determined using computational modelling, and then used to elucidate the binding mechanism of the corresponding sensor complexes. Several molecules were produced that respond to important organic analytes, such as glucose and fenthion, an organophosphorus pesticide. Glucose is an exceedingly important biological …

Towards The Synthesis Of An Artificial Fluorescent Siderophore, Ashley Burns

Honors Theses

Siderophores are molecules capable of binding ferric ions with high affinity (Ka = 1052). This thesis outlines our attempts to synthesize an artificial siderophore, which incorporates a signaling group to help monitor the uptake of ferric ions. The artificial siderophore is a tripodal molecular receptor synthesized in a five-step procedure with a proposed final sixth step. Rhodamine 6G azide (95.0% yield) was formed from rhodamine 6G and the synthesis of 2-azidoethanamine was modified from the literature. The tripodal arm portion of the sensor was successfully synthesized by protecting the catechol of 2,3-dihydroxybenzaldehyde to form 3-formyl-1,2-phenylene dimethanesulfonate (98.8% yield). The reduction …

Construction Of G-Quadruplexes Via Self-Assembly: Enhanced Stability And Unique Properties, Ying He

USF Tampa Graduate Theses and Dissertations

This dissertation mainly contains three parts: 1) The construction of well-defined G8-octamers through the monomer conformational design. 2) The construction of cross-layer interactions in the G8-octamer for enhanced stability in H-bond competitive solvents. 3) Design and synthesis of 8-triazole guanosine with photoluminescent properties.

Through the structural conformational design, we have developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (2’,3’-isopropylidene). This unique design has led to the formation of the first discrete G8-octamer with structure characterized by NMR, MS and single crystal X-ray diffraction. The selectivity between monovalent (K+) and divalent cat-ions (Ba2+ and Sr2+) …

Effects Of Electrical Stimulation On Glioma Cells In Vitro With Implications For Treating Chronic Pain: Development Of A Model System, David C. Platt

Theses and Dissertations

Glial cells comprise over 70% of the central nervous system cells and exhibit diverse functions including regulation of synaptic transmission, neuron protection/repair, maintenance of neuronal metabolism, and are implicated in the development of persistent neuropathic pain. In addition, a perturbation in the concentration of intracellular reactive oxygen species (ROS) and reactive nitrogen species (RNS) has likewise been associated with the development of a chronic pain state. This perturbation in ROS/RNS creates an environment of oxidative stress. However, the mechanism by which the pain signal transmission is modulated, and the roles ROS play in the perpetuation of the pain state are …

Oleic Acid Vesicles: Formation, Mechanisms Of Reactivity, And Uses In Determination Of Terpene Activity, Laura A. Walther

Theses and Dissertations--Chemistry

This dissertation will focus on the volatile compounds released upon the burning of incense which are numerous and varied. The first part of this dissertation is the gas chromatography-mass spectral (GC-MS) analysis of burning incense collected via solid phase microextraction (SPME) with the aim of developing a library of compounds found in incense as used in the Orthodox church.

The second part of this dissertation has the aim of developing a method for forming oleic acid bilayer vesicle membranes and a fluorescence spectroscopy method by which the reactivities of these vesicles can be analyzed. These reactivities include permeability, fluidity, aggregation, …

Design, Synthesis, And Evaluation Of Novel Protease-Activated Receptor 2 (Par2)-Targeting Imaging Agents For Cancer, Jordan C. Lesarge

Electronic Thesis and Dissertation Repository

Aberrant function and over-expression of protease-activated receptor 2 (PAR2), a GPCR, is associated with various cancers and inflammatory diseases. PAR2-targeting ligands have been developed with therapeutic applications but the development of imaging probes is lacking. A series of PAR2-targeted fluorescent and ¹⁸F-PET imaging agents were synthesized and assessed for PAR2-binding. A novel dye-conjugated peptide, Isox-Cha-Chg-ARK(Sulfo-Cy5)-NH₂ (EC₅₀=16nM, K_D=38nM), showed >10-fold increase in potency and binding affinity for PAR2 compared to the leading known fluorescent probe. A novel PET imaging ¹⁸F-labeled peptide, Isox-Cha-Chg-AR-Dpr([¹⁸F]4-FB)-NH₂, is the first PAR2-targeted in vivo imaging agent. …

The Development Of Metal Complexes As Components Of Fluorescent And Nuclear Imaging Probes, William Turnbull

Electronic Thesis and Dissertation Repository

The advent of molecular imaging as a discipline has drastically improved our ability to understand the biochemical and cellular events that drive life, death and disease. This thesis will document the discovery of new metal chelators for Re/^99mTc, new methods of incorporating these metals into peptide structures, as well as new fluorescent compounds. These novel methods and compounds may be used in the development of molecular imaging probes for single photon emission computed tomography (SPECT) and optical imaging techniques, with applications for differentiating cancerous tissue from benign and healthy.

Chapter 2 discusses the development of a dual modality …

Fluorescently Labeled Sirnas And Their Theranostic Applications In Cancer Gene Therapy, Stephen David Kozuch

Seton Hall University Dissertations and Theses (ETDs)

Gene therapy has emerged as a promising precision nano-medicine strategy in the treatment of numerous diseases including cancer. At the forefront of its utility are the applications of short-interfering RNA (siRNA), that silence oncogenic mRNA expression leading to cancer cell death through the RNA interference (RNAi) pathway. Despite the therapeutic potential, siRNAs are limited by poor pharmacological properties, which has hindered their translation into the clinic. Recent studies, however, have highlighted the applications of modified siRNAs, including the use of fluorescent probes and siRNA nanostructures in cancer detection and treatment. The siRNAs reported in this thesis are designed to target …

Synthesis And Characterization Of Fluorescent Nanojars, Vageesha Warnajith Liyana Gunawardana

Masters Theses

Self-assembly is a powerful tool utilized by synthetic chemists to create large, intricate structures for a variety of applications such as drug delivery, adaptable materials and electronics. In contrast to stepwise synthesis, this process allows the formation of intricate molecular architectures starting from synthetically rudimentary building blocks. Nanojars are class of self-assembling, cyclic copper(II) pyrazolate coordination compounds that encapsulate oxoanions with negative two or three charge. The strong anion binding characteristics of nanojars have potential towards developing novel tools for detecting biologically and environmentally relevant anions such as carbonate, sulfate and phosphate.

This work addresses the design and synthesis of …

Fluorescent Probes And Functionalized Nanoparticles For Bioimaging: Synthesis, Photophysical Properties And Applications, Xinglei Liu

Dissertations

The development of new organic molecular probes with excellent photophysical properties and high fluorescence quantum yields is of considerable interest to many research areas including one- and two-photon fluorescence microscopy, fluorescence-based sensing methodologies, and cancer therapy. Series of organic linear-/non-linear optical molecules including squaraine derivatives, and fluorene derivatives as well as other bioconjugates are designed and synthesized during the doctoral study for the aim of ion detection (Chapter 5), photo dynamic therapy, and deep-tissue imaging (Chapter 4). These optical probes are capable of absorbing light in the near infrared (NIR) window and thus have deeper penetration and cause less photodamage …

Tumor-Targeting Fluorinated Phthalocyanines For Theranostic Applications, Erik Nathaniel Carrión

Seton Hall University Dissertations and Theses (ETDs)

Hydrocarbon-based therapeutics and imaging agents are prone to chemical oxidation and degradation resulting in loss of activity and limited functional utility. Thus, more material is required to achieve long-lasting therapeutic effects. Phthalocyanines (Pcs) and their metal complexes (PcMs) can be utilized as prodrugs requiring only renewable energy resources namely, air and light, for cancer therapy and diagnostic (theranostic) applications related to photodynamic therapy (PDT). Replacement of labile C-H bonds in the Pc scaffold with a combination of fluoro and perfluoroisopropyl groups has resulted in a stable yet reactive oxidation catalyst of biological significance and importance. For example, F₆₄PcZn, …

Assessment Of The Viability Of Microwell Plates As Sample Holders For Analytical Excitation-Emission Spectroscopy Of Polyaromatic Hydrocarbons In 75% Ethanol, Lauren M. Ridley-Hoffman

Seton Hall University Dissertations and Theses (ETDs)

Polyaromatic hydrocarbons (PAHs) in the environment are a significant concern as many compounds in this class are potential carcinogens. PAHs resulting from petroleum spills can contaminate natural waters and the products obtain from them (fish and fish products in particular). Previous studies by Pena, et. al. on ethanolic extracts of organs from menhaden captured in the vicinity of the Deepwater Horizon (Macondo oil well) spill have shown that fluorescence excitation spectroscopy is a useful technique for detecting the presence of PAH metabolites and fluorescent vitamins. The study has also concluded that previous methods for analyzing PAHs using fluorescence spectroscopy used …

Higher Energy Gap Control Of Fluorescence In Conjugated Polymers, Chien-Hung Chiang

LSU Doctoral Dissertations

Chemo- and biosensors based on fluorescent conjugated polymer benefit from greater detection sensitivity due to amplification of the electronic perturbations produced by analyte binding. This amplification stems from the exciton-transporting properties of conjugated polymers. A conventional design paradigm relies on the analyte binding events which generate sites of lower energy relative to the polymer energy: either fluorescence quenching sites (turn-off sensors) or bathochromically shifted fluorophores (turn-on sensors). In both type sensors, the excitons migrate to the lower-energy site created by analyte binding.

This dissertation primarily focused the investigation of an alternative paradigm when analyte binding creates higher energy gap sites …