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Cyanine Dyes Targeting G-Quadruplex Dna: Significance In Sequence And Conformation Selectivity, Hang T. Huynh

Chemistry Theses

Small molecules interacting with DNA is an emerging theme in scientific research due to its specificity and minimal side-effect. Moreover, a large amount of research has been done on finding compounds that can stabilize G-quadruplex DNA, a non-canonical secondary DNA structure, to inhibit cancerous cell proliferation. G-quadruplex DNA is found in the guanine-rich region of the chromosome that has an important role in protecting chromosomes from unwinding, participate in gene expression, contribute in the control replication of cells and more. In this research, rationally designed, synthetic cyanine dye derivatives, which were tested under physiologically relevant conditions, were found to selectively …

Spectroscopic Investigation Into Minor Groove Binders Designed To Selectively Target Dna Sequences, Joseph Walton

Chemistry Theses

Recently, there has been increasing focus toward the development of small molecules designed to target a specific sequences of double stranded DNA for therapeutic purposes¹. Minor groove binding compounds have been shown to be capable of selectivity target GC sites in AT tract DNA². In this research, binding selectivity was investigated using absorption, fluorescence and circular dichroic properties of selected DB minor groove binders in the presence of two unique DNA sequences. Further insight was gained by comparing the electrostatic potential maps and optimized structures of the compounds of interest. Using the results presented, potential selective …

Fabrication, Characterization, And Application Of Carbon Nanoparticles For The Detection Of Heavy Metal Ions In Aqueous Media, Aaron Michael Simpson

MSU Graduate Theses

This research set out to develop a method for producing Carbon nanoparticles (CNPs) from glycerol and use them to detect Cu2+, Hg2+, and Pb2+ ions in aqueous solution. Three synthesis methods were developed using the following mixtures: (1) glycerol and silica, (2) glycerol, silica, and H3PO4, and (3) glycerol with H3PO4. The structure of the particles was characterized using a variety of spectroscopic techniques. Size distributions were obtained from scanning electron microscopy images. The particles were spherical with average diameters of 66, 58, and 89 nm respectively and believed to consist of a carbon core with carboxylic acid and alcohol …

A Platform For Fast Detection Of Let-7 Micro Rna Using Polyaniline Fluorescence And Image Analysis Techniques, Partha P. Sengupta

Master's Theses

The project describes a new strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10^-11 M (10 pM) of target oligonucleotides could be detected within 15 minutes of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to …

Influence Of Shelling Temperature And Time On The Optical And Structural Properties Of Cuins2/Zns Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

CIS/ZnS core/shell QDs are an important class of nanomaterials for optoelectronic, photovoltaic and photoluminescence applications. They consist of lower toxicity materials than the prototypical II-VI Cd-based QDs and show long fluorescence lifetimes, which generates prospective in biological imaging applications. It is vital to develop reproducible synthetic methods for this new class of nanomaterials in order to maintain small sizes with high QYs. CIS core QDs have been shelled with ZnS at various temperatures from 90-210°C for reaction times ranging from 20-140 minutes to examine the role of thermodynamics and kinetics on the shell growth. Using HR-TEM and ICP-MS, it was …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

Design, Synthesis And Study Of Novel Nucleobase Analogs, Augusto Matarazzo

Electronic Thesis and Dissertation Repository

This thesis focused on nucleobase modified peptide nucleic acid (PNA) and DNA to expand the repertoire of available nucleobase analogs used in the study of nucleic acids. More specifically, we are interested in modification of the nucleobases such that they retain their ability to undergo Watson-Crick base pairing. Moreover, our goal is to modify the nucleobases in order to engender them with useful photophysical properties such that they may be used as biomolecular tools to investigate nucleic acid structure and dynamics.

To that end, a derivative of 5-aminouracil (5-AU) labelled with the amine-reactive chromophore 9-chloroacridine was prepared for the purpose …

Using Fluorescence – Polarization Endoscopy In Detection Of Precancerous And Cancerous Lesions In Colon And Pancreatic Cancer, Tauseef Charanya

McKelvey School of Engineering Theses & Dissertations

Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real time detection of these lesions. Utilizing a new thermoresponsive sol-gel formulation with targeted molecular probe allowed topical application and detection of precancerous and cancerous lesions during endoscopy. Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy served as a validation strategy prior to obtaining biopsies.

In order to reduce repeat surgeries arising from incomplete tumor …

Structural And Functional Analysis Of The Reaction Center Complexes From The Photosynthetic Green Sulfur Bacteria, Guannan He

Arts & Sciences Electronic Theses and Dissertations

The reaction center (RC) complex of the green sulfur bacterium Chlorobaculum tepidum is composed of the Fenna-Matthews-Olson (FMO) antenna protein and the reaction center core (RCC) complex. The RCC complex has four subunits: PscA, PscB, PscC, and PscD. The structure of the intact and functional FMO-RCC complex was studied by chemically cross-linking the purified sample followed by biochemical and spectroscopic analysis. The interaction sites of the cross-linked complex were also studied using LC-MS/MS. A structural model is proposed based on those results. In addition, the RCC complexes were purified, both the PscA-PscC complex from the Chlorobaculum tepidum and the PscA-PscB …

Amylin Structure, Aggregation And Pancreatic Β Cell Toxicity, Sharadrao Patil

Doctoral Dissertations

In most type 2 diabetes patients, amyloid plaques have been found juxtaposed with membranes of pancreatic β-cells. These plaques are composed of amyloid fibrils of the 37 residue endocrine hormone amylin and cause distinct changes in cell membrane morphology associated with the destruction of β-cells. Research is still ongoing to identify the toxic species involved and the mechanisms by which mature fibrils or oligomers cause cytotoxicity. The projects undertaken were designed to study the molecular structural features of amylin, mechanism of amyloid aggregation and, to develop cytotoxicity inhibitors. We determined the structure of human amylin bound to SDS micelles using …

Development And Validation Of An Optically-Based Strain Measuring Orthopaedic Screw For Fracture Fixation Implants, Nakul Ravikumar

All Theses

In the USA over 28 million musculoskeletal injuries are treated annually, including 2 million fracture fixation surgeries (about 0.5% of the population).[1] Treatment of large osseous defects use allografts which have failure rates of up to 25%, and complication rates as high as 30-60%.[2] Fracture fixation usually involves mechanical fixation with rods, plates and/or screws which repair slowly and are susceptible to infection. Implant infection and loosening are serious concerns, but can currently only be measured through expensive instrumented implants, biopsy culture, or radiographs. However, none of these directly quantify implant loading and stability. There is therefore a need for …

A Non-Invasive Fluorescence-Based Oxygen Sensor And Platform For Studying Cell Responses To Metabolic Agents In Real-Time, Koutilya Reddy Buchapudi

Doctoral Dissertations

A fluorescence-based sensor in a transverse flow/stop measurement platform has been developed to determine real-time changes in oxygen consumption rates for cell metabolic studies. The oxygen sensitive fluorophore platinum octaethylporphyrin was embedded in a cellulose acetate matrix and affixed to a fiber optic bundle, which provided for transmission of the excitation and emission wavelengths of the film. The fiber optic bundle was sealed in a sensor head that can be used in standard 24-well plates common to research labs. The utility of the sensor and sensing platform were determined by measuring the changes in oxygen consumption rates of Candida albicans …

Synthesis And Functionalization Of Fluorescent Quantum Dot Bioconjugates For Cellular Imaging Of Directed Gene Therapy, Jason Matthew Davis

MSU Graduate Theses

Herein, I optimize a method for synthesis and bioconjugation of water-soluble, fluorescent CdSe/ZnS quantum dots (QDs) for targeted cellular delivery of DNA. Core CdSe QDs were synthesized in high temperature organic solvents and passivated with a ZnS shell to increase quantum yield. The fluorescent QD nanoparticles were made water-soluble by enveloping them with an amphiphilic polymer. These aqueous nanoparticles were functionalized with tertiary amines to impart a positive charge, allowing electrostatic binding to negatively-charged DNA. The conjugated QDs were characterized using zeta potential and electrophoresis to gauge their ability to electrostatically bind DNA. The QDs were further modified by conjugation …

The Use Of Cod, Toc, Fluorescence, And Absorbance Spectroscopy To Estimate Biochemical Oxygen Demand In Wastewater, Evelyn Aramaine Christian

UNLV Theses, Dissertations, Professional Papers, and Capstones

All wastewater treatment facilities must obtain a National Pollution Discharge Elimination System (NPDES) permit, which regulates the quality of water that is discharged. Common to all NPDES permits is a limit on organic matter, as determined by the five-day biochemical oxygen demand (BOD5) test. More rapid methods, such as chemical oxygen demand (COD), total organic carbon (TOC), fluorescence, and absorbance spectroscopy are also capable of quantifying organic matter. Previous studies indicate it is possible to develop correlations between these parameters. This study explored the correlations using influent, primary clarifier effluent, and finished effluent samples from an operational wastewater treatment plant …

Design And Development Of Bodipy-Based Fluorescent Probes For Sensing And Imaging Of Cyanide, Zn (Ii) Ions, Lysosomal Ph And Cancer Cells, Jingtuo Zhang

Dissertations, Master's Theses and Master's Reports - Open

BODIPY (4,4-Difluoro-3a,4a-diaza-s-indacene) dyes have gained lots of attention in application of fluorescence sensing and imaging in recent years because they possess many distinctive and desirable properties such as high extinction coefficient, narrow absorption and emission bands, high quantum yield and low photobleaching effect. However, most of BODIPY-based fluorescent probes have very poor solubilities in aqueous solution, emit less than 650 nm fluorescence that can cause cell and tissue photodamages compared with bio-desirable near infrared (650-900 nm) light. These undesirable properties extremely limit the applications of BODIPY-based fluorescent probes in sensing and imaging applications. In order to overcome these drawbacks, we …

Purification And Characterization Of Bcsc; An Integral Component Of Bacterial Cellulose Export, Emily D. Wilson Ms

Theses and Dissertations (Comprehensive)

Biofilms are a growing concern in the medical field due to their increased resistance to antibiotics. When found in a biofilm, bacteria can have antibiotic resistance 10-1000 times that of their planktonic counterparts. Therefore, it is important to study the formation of biofilms. Cellulose biofilms are formed by Enterobacteriaceae, such as many Escherichia coli and Salmonella spp. strains. Biofilms provide these species with benefits including antimicrobial protection, development of bacterial communities, promotion of DNA exchange, uptake of nutrients, and, in the case of cellulose biofilms, immune system evasion. Cellulose biofilms are controlled by the Bacterial cellulose synthesis (Bcs) complex located …

Biophysical Characterization Of The Folding, Membrane Topology And Ion Transport Activity Of Ucp2 Using Selective Trp Mutants, Tyler C. Auld

Theses and Dissertations (Comprehensive)

Human Uncoupling Protein 2 (hUCP2) is one of five known human UCPs which are found in the inner mitochondrial membrane and have been shown to facilitate the translocation of protons from the intermembrane space to the mitochondrial matrix. The detailed physiological role of UCP2 proton transport, the mechanism by which it mediates this proton transport, as well as its structure has also yet to be elucidated. In order to help determine the topology of UCP2 embedded in the membrane as well as its mechanism of proton transport, the intrinsic fluorescence properties of the two tryptophan residues (Trp) present in its …

The Role Of Protein Structure Conformational Change In Secondary Functions Of Threonyl-Trna Synthetase, Shawn Bruce Egri

UVM College of Arts and Sciences College Honors Theses

Traditionally, threonyl-tRNA synthetase (ThrRS) has been studied for its canonical function of aminoacylation. Recently, however, the enzyme has been identified as a potent angiogenic factor. Both functions are influenced by a structural change within the enzyme. Upon binding of a specific inhibitor, borrelidin (BN), an alternative conformation is adopted, preventing angiogenic function. Mutant versions of ThrRS were generated using site-directed mutagenesis to mimic the BN-bound structure. The effects of these mutations on threonine-induced conformational changes were explored using steady state fluorescence. The greatest conformational impairment was seen with A460S and S488W which demonstrated 38% and 41% of the control response, …

Heterosandwich Assay Of Nicotinic Acetylcholine Receptors, Augustine J. Pagan Iv

Theses and Dissertations

Using the technology afforded by Winschel et al., cyclen-1, a high affinity, strong complexation agent for 8-hydroxypyrene-1,3,6 trisulfonate and derivatives, a new assay has been developed for fluorescently labeling proteins of interest (POIs). Ligation of the endogenous ligand for nicotinic acetylcholine receptors (nAChRs), acetylcholine, using click chemistry afforded the triazole derivative of an alkynyl-acylcholine (compound 1) with 8-azidopyrene-1,3,6 trisulfonate (compound 2). Liposomes encapsulated with Rhodamine B were used to strengthen the initial fluorophore response of compound 2, using an anchored form of cyclen-1 complex. Using a palmitoyl tail as the lipophilic moiety for liposomal amplification, the …