Physical Sciences and Mathematics Commons^™

Novel Near-Infrared Cyanine Dyes For Fluorescence Imaging In Biological Systems, Nilmi T. Fernando

Chemistry Dissertations

Heptamethine cyanine dyes are attractive compounds for imaging purposes in biomedical applications because of their chemical and photophysical properties exhibited in the near-infrared region. A series of meso amino-substituted heptamethine cyanine dyes with indolenine, benz[e]indolenine and benz[c,d]indolenine heterocyclic moieties were synthesized and their spectral properties including fluorescence quntum yield were investigated in ethanol and ethanol/water mixture. Upon substitution with amines, the absorption maxima of the dyes shifted to the lower wavelength region (~600 nm), showed larger Stokes shifts and stronger fluorescence which can be attributed to an excited state intramolecular charge transfer (ICT). High quantum yields …

Nucleic Acid Substrates: Investigation Of Structural And Dynamic Features That Influence Enzyme Activity, Christopher N. Johnson

Chemistry Dissertations

The previous view of DNA as a linear sequence of bases is evolving to consider structure, topology and dynamics. Sequences surrounding damage lesions have been shown to effect enzyme recognition and processing. Here we present an in depth investigation of subtle structural and dynamical features imparted to nucleic acid duplexes by a designed modification or damage lesions. Highly restrained solution structures were generated and validated utilizing a range of NMR techniques. This allowed for the characterization of multiple features of the nucleic acid duplex; such as base pairing, backbone torsion angles, deoxyribose sugar pucker, and intra and inter nucleotide proton …

Development Of Boronic Acid Flurescent Reporters, Boronic Acid-Modified Thymidine Triphosphates For Sensor Design And Antagonists Of Bacterial Quorum Sensing In Vibrio Harveyi, Yunfeng Cheng

Chemistry Dissertations

Carbohydrates are known to play important roles in a large number of physiological and pathological processes. Conceivably, “binders” of carbohydrates of biological importance could be used as diagnostic and therapeutic agents. Currently, lectins are the major available tools in research for carbohydrate recognition. However, the available lectins often have cross-reactivity issues, along with the high costs and stability issues. Therefore, there is a critical need to develop alternatives (lectin mimics). In this regard, there have been very active efforts in developing different “binders”, such as small molecule lectinmimics and aptamers. Among all the small molecule lectinbmimics developments, boronic acid stands …

I. Synthesis Of Anthraquinone Derivatives For Electron Transfer Studies In Dna. Ii. Characterization Of The Interaction Between Heme And Proteins., Yu Cao

Chemistry Dissertations

Anthraquinone (AQ) derivatives with relatively high reduction potentials have been synthesized to afford good candidates for electron transfer studies in DNA. Electron withdrawing groups on the anthraquinone ring gave derivatives with less negative reduction potentials. The anthraquinone imide (AQI) derivatives had reduction potentials less negative than AQ derivatives. The AQI ring system was subject to base-induced hydrolysis.

Water-soluble sulfonated tetraarylporphyrins have been studied in a wide variety of contexts. Herein, we report the first synthesis of a pentasulfonated porphyrin bearing an internal cyclic sulfone ring. Treatment of 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4) with fuming H₂SO₄ gave a structure consistent with …

Tuning Calcium Bindging Affinities With Related Biological Functions Of Calmodulin And Designing Protein Based Contrast Agent, Jie Jiang

Chemistry Dissertations

Calmodulin (CaM) is a ubiquitous intracellular protein that regulates biological activities of numerous enzymes and ion channels. Upon responding Ca²⁺ concentration change, Ca²⁺- dependent CaM activates the hydrolyzation of cGMP by PDE and Ca²⁺ releasing channel activity of ryanodine receptor. In this dissertation, a series of CaM variants were engineered to enhance Ca²⁺ binding affinities by increasing the number of negative charged residues in individual EF-hand. The capability of shifting the biphasic Ca²⁺-activation profile of RyR1 is significantly altered by changing Ca²⁺ binding affinity of CaM at the C-terminal. This indicates that …

Mechanistic Studies Of Two Selected Flavin-Dependent Enzymes: Choline Oxidase And D-Arginine Dehydrogenase, Hongling Yuan

Chemistry Dissertations

Choline oxidase catalyzes the flavin-dependent, two-step oxidation of choline to glycine betaine via the formation of an aldehyde intermediate. The oxidation of choline includes two reductive half-reactions followed by oxidative half-reactions. In the first oxidation reaction, the alcohol substrate is activated to its alkoxide via proton abstraction and oxidized via transfer of a hydride from the alkoxide α-carbon to the N(5) atom of the enzyme-bound flavin. In the wild-type enzyme, proton and hydride transfers are mechanistically and kinetically uncoupled.

The role of Ser101 was investigated in this dissertation. Replacement of Ser101 with threonine, alanine, cysteine, or valine demonstrated the importance …

Development Of Inhibitors And Assay Methods For Histone Acetyltransferases, Jiang Wu

Chemistry Dissertations

Histone acetyltransferases (HATs) are important enzymes in transcriptional control and potential targets for chemotherapeutic intervention in malignant diseases. Among different HAT members, the yeast Esa1 and human Tip60 (the HIV-1 Tat interactive protein, 60KDa) play multiple roles in normal cellular processes including transcription, cell cycle and checkpoint machinery, double strand DNA break repair, apoptosis, and cell cycle progression. Tip60 is also implicated in several human diseases such as prostate cancer, and gastric cancer. These studies suggest that Tip60 is a potential therapeutic target for new cancer treatment. So, we designed experimental work to synthesize and investigate organic inhibitors of Tip60 …

Defining A Molecular Mechanism For Lead Toxicity Via Calcium-Binding Proteins, Michael Kirberger

Chemistry Dissertations

Essential metals like Ca²⁺ and Zn²⁺ play critical roles in biological processes through protein interactions. Conversely, non-essential metals (e.g., Gd³⁺ and Pb²⁺) also interact with proteins, often with toxic effects. Molecular metal toxicity is assumed to be due to ionic displacement, and studies have demonstrated that Pb²⁺ replaces Zn²⁺, Ca²⁺ and other essential metals in proteins. The focus of this work was to compare protein Ca²⁺ and Pb²⁺ -binding sites and to investigate a mechanism of Pb²⁺ toxicity in Ca²⁺-binding proteins, particularly the intracellular trigger protein …

Protein-Nucleic Acid Interactions In Nuclease And Polymerases, Abdur Rob

Chemistry Dissertations

DNA polymerase binds to the double stranded DNA and extends the primer strand by adding deoxyribonucletide to the 3’-end. Several reactions in the polymerase active site have been reported by Kornberg in addition to the polymerization. We observed DNA polymerase I can act as a pyrophosphatase and hydrolyze deoxyribonucletide. In performing the pyrophosphatase activity, DNA polymerase I requires to interact with RNA. RNA in general, was found to activate the DNA polymerase I as pyrophosphatase. This hydrolysis causes depletion of dNTP and inhibits DNA polymeration synthesis in vitro. In this RNA-dependent catalysis, DNA polymerase I catalyzes only dNTP but …

On The Biochemistry, Mechanism And Physiological Role Of Fungal Nitronate Monooxygenase, Kevin Francis

Chemistry Dissertations

Nitronate monooxygenase (E.C. 1.13.11.16), formerly known as 2-nitropropane dioxygenase (EC 1.13.11.32), is a flavin dependent enzyme that catalyzes the oxidation of nitronates to their corresponding carbonyl compounds and nitrite. Despite the fact that the enzyme was first isolated from Neurospora crassa 60 years ago, the biochemical and physiological properties of nitronate monooxygenase have remained largely elusive. This dissertation will present the work that established both the catalytic mechanism and physiological role of the fungal enzyme.

The biological and biochemical properties of propionate-3-nitronate, the recently discovered physiological substrate for nitronate monooxygenase, will be extensively reviewed. The nitronate is produced by a …