Digital Commons Network^™

Myricetin Inhibits Escherichia Coli Dnab Helicase But Not Primase, Mark A. Griep, Sheldon Blood, Marilynn A. Larson, Scott A. Koepsell, Steven H. Hinrichs

Mark A. Griep Publications

Primase and DnaB helicase play central roles during DNA replication initiation and elongation. Both enzymes are drug targets because they are essential, persistent among bacterial genomes, and have different sequences than their eukaryotic equivalents. Myricetin is a ubiquitous natural product in plants that is known to inhibit a variety of DNA polymerases, RNA polymerases, reverse transcriptases, and telomerases in addition being able to inhibit kinases and helicases. We have shown that myricetin inhibits Escherichia coli DnaB helicase according to a mechanism dominated by noncompetitive behavior with a K_i of 10.0 ± 0.5 μM. At physiological ATP concentration, myricetin inhibits …

Counter-Flow Ion Mobility Analysis: Design, Instrumentation, And Characterization, Nosa Agbonkonkon

Theses and Dissertations

The quest to achieve high resolution in ion mobility spectrometry (IMS) has continued to challenge scientist and engineers in the field of separation science. The low resolution presently attainable in IMS has continued to negatively impact its utility and acceptance. Until now, efforts to improve the resolution have mainly focused on better instrumentation and detection methods. However, since the resolution of IMS is diffusion limited, it makes sense to address this limitation in order to attain high resolution. This dissertation presents a new IMS technique, which utilizes a high electric field and opposing high gas flow velocity with the aim …

Assemblies Of Assemblies: Supramolecular Ordering Of Nanoscopic Ruthenium Polypyridyl Building Blocks, Kelly Lyle Wouters

Chemistry & Biochemistry Dissertations - Archive

Biological systems have long since perfected the development of nanoengineering. Cellular structure and machinery is based, to a significant extent, on the formation of nanometer to micron-sized assemblies of proteins. These architectures start with unique primary, secondary, tertiary, and quaternary structural complexity and can be constructed from a relatively simple set of building blocks. Using this strategy as inspiration, assemblies based on [Ru(phenanthroline)3]2+ building blocks have been synthesized forming polyruthenium species bridged by the tpphz (tetrapyrido[3,2-a:2’,3’-c:3’’,2’’-h:2’’’,3’’’-j]phenazine) and tatpp (9,11,20,22- tetraaza tetrapyrido[3,2-a:2’,3’-c:3’’,2’’-l:2’’’’,3’’’’-n]-pentacene) ligands. Importantly, these assemblies exhibit unique hierarchical structural components which arise directly from the chirality inherent in the octahedral …

⁵⁷Fe Mössbauer Spectral And Muon Spin Relaxation Study Of The Magnetodynamics Of Monodispersed Γ-Fe₂O₃ Nanoparticles, Leïla Rebbouh, Raphäel P. Hermann, Fernande Grandjean, Taeghwan Hyeon, Kwangjin An, Alex Amato, Gary J. Long

Chemistry Faculty Research & Creative Works

The Mössbauer spectra of monodispersed iron oxide nanoparticles with diameters of 4, 7, 9, and 11 nm have been measured between 4.2 and 315 K and fitted within the formalism for stochastic fluctuations of the hyperfine Hamiltonian. In this model, the hyperfine field is assumed to relax between the six ±x, ±y, and ±z directions in space with a distribution of relaxation rates that is temperature dependent. Muon spin relaxation measurements have been carried out on the 9 nm particles between 4.2 and 295 K. Both techniques reveal three regimes in the magnetic dynamics of these nanoparticles. In the low-temperature …

A Strategy To Protect And Sensitize Near-Infrared Luminescent Nd3+ And Yb3+: Organic Tropolonate Ligands For The Sensitization Of Ln3+-Doped Nayf4 Nanocrystals, Jian Zhang, Chad M. Shade, Demetra A. Chengelis, Stéphane Petoud

Department of Chemistry: Faculty Publications

A strategy to sensitize and protect near-infrared (NIR) emitting Nd³⁺ and Yb³⁺ is presented. Combining protection provided by the inorganic matrix of NaYF₄ nanocrystals and sensitization from tropolonate ligands capped on their surface, the lanthanide cation centered luminescence was observed through the ligand excitation. The extended lanthanide luminescence lifetimes indicate the success of this strategy.

An Overview Of The Genus Nardostachys, Asima Chatterjee, Utpal Dutta, Debasish Bandyopadhyay, Anupam Nayak, Bidyut Basak, Avijit Banerji, Julie Banerji

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Nardostachys jatamansi, a medicinally important herb of Nepalese origin, has been used for centuries in the Ayurvedic and Unani systems of medicine. In combination with Marsilea minuta it is being used as an antistress and anticonvulsant drug and also finds use in the treatment of epilepsy. Recently, it has been reported that N. jatamansi, which plays an important role in protecting from cerebral ischemia and liver damage, is also used for the treatment of osteoporosis and hypercalcemia. The other member of the genus Nardostachys, N. chinensis, possesses antifungal and antimalarial properties. It is also used in the treatment of skin …

Structure Of Arabidopsis Thaliana 5-Methylthioribose Kinase Reveals A More Occluded Active Site Than Its Bacterial Homolog, Shao Yang-Ku, Kenneth A. Cornell, P. Lynne Howell

Chemistry and Biochemistry Faculty Publications and Presentations

Background: Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics.

Results: The structure of Arabidopsis thaliana MTR kinase co-crystallized with ATPγS and MTR has been determined at 1.9 Å resolution. The structure is similar to B. subtilis MTR kinase and has the same protein kinase fold observed in other evolutionarily related …

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of …

The Characterization Of Trna Modifying Enzymes S-Adenosylmethionine : Trna Ribosyltransferase-Isomerase (Quea) And A Novel Type I Gtp Cyclohydrolase, Shilah Amal Bonnett

Dissertations and Theses

Queuosine is a hypermodified nucleoside located in the wobble position of bacterial and eukaryotic tRNAs coding for Asp, Tyr, His and Asn. The biosynthesis involves the participation of S-adenosyl-methionine:tRNA ribosyltransferase-isomerase (QueA) and a GTP Cyclohydrolase-I. QueA catalyzes the transfer and isomerization of the ribosyl moiety from AdoMet to preQ1 modified tRNA. Substrate analogs of AdoMet were used to elucidate important substrate-enzyme interactions and to test key steps in the proposed chemical mechanism. Replacing AdoMet with SeAdoMet had little effect upon substrate binding but exhibited 30-fold reduction in kcat, consistent with deprotonation at C-5' as the first catalytic step. 7-deazaAdoMet failed …

Microcantilever Surface Modification For Chem-/Bio-Sensing, Hongwei Du

Doctoral Dissertations

One focus of the microcantilever (MCL) sensing area is to develop a novel surface modification approach to increase the microcantilever bending amplitudes and thus further improve sensitivities. In this dissertation, enzyme incorporated using the Layer by-Layer (LbL) process, LbL deposition of micro-, nano-hydrogel particles and electrophoretic deposition (EPD) of micro-, nano-hydrogel particles were applied to prepare a multilayer or thin hydrogel films on the surface of microcantilevers. Prior to applying to the microcantilevers, LbL and electrophoretic deposition techniques were also applied to gold coated silicon wafer surfaces to investigate the feasibility and deposition behavior using these techniques. The multilayers prepared …

Instrumentation And Metrology For Single Rna Counting In Biological Complexes Or Nanoparticles By A Single-Molecule Dual-View System, Hui Zhang, Dan Shu, Faqing Huang, Peixuan Guo

Faculty Publications

Limited by the spatial resolution of optical microscopy, direct detection or counting of single components in biological complexes or nanoparticles is challenging, especially for RNA, which is conformationally versatile and structurally flexible. We report here the assembly of a customized single-molecule dual-viewing total internal reflection fluorescence imaging system for direct counting of RNA building blocks. The RNA molecules were labeled with a single fluorophore by in vitro transcription in the presence of a fluorescent AMP. Precise calculation of identical or mixed pRNA building blocks of one, two, three, or six copies within the bacteriophage phi29 DNA packaging motor or other …

The Tropical Forest And Fire Emissions Experiment: Trace Gases Emitted By Smoldering Logs And Dung From Deforestation And Pasture Fires In Brazil, Ted J. Christian, Robert J. Yokelson, João A. Carvalho, David W.T. Griffith, Ernesto C. Alvarado, José Carlos Santos, Turibio Gomes Soares Neto, Carlos A.Gurgel Veras, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Earlier work showed that Amazonian biomass burning produces both lofted and initially unlofted emissions in large amounts. A mobile, Fourier transform infrared spectrometer (FTIR) measured the unlofted emissions of 17 trace gases from residual smoldering combustion (RSC) of logs as part of the Tropical Forest and Fire Emissions Experiment (TROFFEE) during the 2004 Amazonian dry season. The RSC emissions were highly variable and the few earlier RSC measurements lay near the high end of combustion efficiency observed in this study. Fuel consumption by RSC was ∼5% of total for a planned deforestation fire. Much regional RSC probably occurs in the …

The Tropical Forest And Fire Emissions Experiment: Emission, Chemistry, And Transport Of Biogenic Volatile Organic Compounds In The Lower Atmosphere Over Amazonia, Thomas Karl, Alex Guenther, Robert J. Yokelson, Jim Greenberg, Mark Potosnak, Donald R. Blake, Paulo Artaxo

Chemistry and Biochemistry Faculty Publications

Airborne and ground-based mixing ratio and flux measurements using eddy covariance (EC) and for the first time the mixed layer gradient (MLG) and mixed layer variance (MLV) techniques are used to assess the impact of isoprene and monoterpene emissions on atmospheric chemistry in the Amazon basin. Average noon isoprene (7.8 +/- 2.3 mg/m(2)/h) and monoterpene fluxes (1.2 +/- 0.5 mg/m(2)/h)compared well between ground and airborne measurements and are higher than fluxes estimated in this region during other seasons. The biogenic emission model, Model of Emissions of Gases and Aerosols from Nature (MEGAN), estimates fluxes that are within the model and …

Oxygen Measurement Via Phosphorescence: Reaction Of Sodium Dithionite With Dissolved Oxygen, Zhimin Tao, Jerry Goodisman, Abdul-Kader Souid

Chemistry - All Scholarship

A homemade instrument for the measurement of oxygen concentration in aqueous solutions measures the decay rate of the phosphorescence of a Pd-porphyrin complex (phosphor) dissolved in the solution, which is flashed every 0.1 s with 630 nm light. The concentration of O ₂ is a linear function of the decay rate. The instrument is used to study the reaction of dithionite (S ₂O ₄ ^2-) with O ₂ at 25°C and 37°C. It is found that the ratio of dithionite to oxygen consumed in the reaction is 1.2 ± 0.2 at 25°C and 1.7 ± 0.1 at 37°C, …

Novel Perturbation Approach For The Structure Factor Of The Attractive Hard-Core Yukawa Fluid, Andrij Trokhymchuk, Roman Melnyk, Filip Moucka, Ivo Nezbeda

Faculty Publications

A novel perturbation approach for the structure factor S(k) of the Lennard-Jones-type Yukawa fluid with z=1.8 is presented. An approach is based on a new reference system, that is, the short-range Yukawa model with z0 > z=1.8. By choosing for the reference system the value z0=6, it is shown that (i) the proposed approach for S(k) performs much better than the traditional hard-sphere reference perturbation method does; (ii) the use of an approximate mean spherical (MSA) description of the reference structure factor provides the results for S(k) that are more accurate as those obtained from the direct MSA computations; and (iii) …

Ovarian Cancer G Protein–Coupled Receptor 1, A New Metastasis Suppressor Gene In Prostate Cancer, Lisam Shanjukumar Singh, Michael Berk, Rhonda Oates, Zhenwen Zhao, Haiyan Tan, Ying Jiang, Aimin Zhou, Kashif Kirmani, Rosemary Steinmetz, Daniel Lindner, Yan Xu

Chemistry Faculty Publications

Background

Metastasis is a process by which tumors spread from primary organs to other sites in the body and is the major cause of death for cancer patients. The ovarian cancer G protein–coupled receptor 1 (OGR1) gene has been shown to be expressed at lower levels in metastatic compared with primary prostate cancer tissues.

Methods

We used an orthotopic mouse metastasis model, in which we injected PC3 metastatic human prostate cancer cells stably transfected with empty vector (vector-PC3) or OGR1-expressing vector (OGR1-PC3) into the prostate lobes of athymic or NOD/SCID mice (n = 3–8 mice per group). Migration of PC3 …

Isolation Of The Saddle And Crown Conformers Of Cyclotriveratrylene (Ctv) Oxime, Marlon R. Lutz Jr., David C. French, Peter Rehage, Daniel P. Becker

Chemistry: Faculty Publications and Other Works

The oxime of cyclotriveratrylene (CTV) has been prepared and the individual crown and saddle conformers were isolated and characterized. The equilibrium constant was measured in CDCl3 and in DMSO-d6 and was shown to favor the crown conformer by an order of magnitude in DMSO-d6, relative to an approximately equal mixture at equilibrium in CDCl3. The time course for interconversion of the saddle to the crown was measured by 1H NMR and the t1/2 of the saddle was determined to be 2.45 h in CDCl3 at 25 °C, and 3.71 h in DMSO-d6.

Organic Geochemical Investigation Of A Highly Contaminated Urban Waterway: The Gowanus Canal, Brooklyn, New York, Usa, Michael A. Kruge, Kevin K. Olsen, Eric A. Stern

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The Gowanus Canal is an industrial waterway constructed in the mid-19^th century by widening and deepening a natural tidal channel. It is ca. 3 km in length and empties into Gowanus Bay, an arm of New York Harbor. Its banks, reinforced by bulkheads and piers, became the site of intensive industrial activity, including oil refining, coal gasification, soap making and tanning. Even though much of the industrial activity along the canal has ceased, its sediments remain highly enriched in organic and inorganic contaminants, with combined sewer outfalls continuing to transport pollutants into the canal. The canal area remains densely …

Aromatase And Cox In Breast Cancer: Enzyme Inhibitors And Beyond, Robert W. Brueggemeier, Bin Su, Yasuro Sugimoto, Edgar S. Diaz-Cruz, Danyetta D. Davis

Chemistry Faculty Publications

Aromatase expression and enzyme activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase (CYP19) gene expression and the expression of cyclooxygenase (COX) genes. Additionally, nonsteroidal anti-inflammatory drugs (NSAIDs) and COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase and/or cyclooxygenases can act locally to decrease the biosynthesis of estrogen and may …

A Novel Empirical Free Energy Function That Explains And Predicts Protein–Protein Binding Affinities, Joseph Audie, Suzanne Scarlata

Chemistry & Physics Faculty Publications

A free energy function can be defined as a mathematical expression that relates macroscopic free energy changes to microscopic or molecular properties. Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to score and discriminate between native and non-native binding modes. However, there is a natural tension between developing a function fast enough to solve the scoring problem but rigorous enough to explain and predict binding affinities. Here, we present a novel, physics-based free energy function that is computationally inexpensive, yet explanatory and predictive. The function results from a derivation …

Thermal Stability Of Nanostructurally Stabilized Zirconium Oxide, Fereydoon Namavar, Gonghua Wang, Chin Li Cheung, Renat F. Sabirianov, Xiao Cheng Zeng, Wai Ning Mei, Jaeil Bai, Joseph R. Brewer, Hani Haider, Kevin L. Garvin

Xiao Cheng Zeng Publications

Nanostructurally stabilized zirconium oxide (NSZ) hard transparent films were produced without chemical stabilizers by the ion beam assisted deposition technique (IBAD). A transmission electron microscopy study of the samples produced below 150 °C revealed that these films are composed of zirconium oxide (ZrO₂) nanocrystallites of diameters 7.5 ± 2.3 nm. X-ray and selected-area electron diffraction studies suggested that the as-deposited films are consistent with cubic phase ZrO₂. Rutherford backscattering spectroscopy (RBS) indicated the formation of stoichiometric ZrO₂. The phase identity of these optically transparent NSZ films was in agreement with cubic ZrO₂, …

Electrochemical Codeposition Of Ha/Collagen Coating And Preliminary In Vitro Tests, Yan-Li Xu, Long-Xiang Lin, Zhi-Wang Geng, Chang-Jian Lin

Journal of Electrochemistry

An electrochemical co-deposition technique has been developed to prepare a hydroxyapatite(HA)/collagen composite coating on Ti substrate.The SEM results show that the composite coating exhibits a homogeneous and porous morphology with nano-micro structure.And the XPS results demonstrate that the composite coating is formed by an organic-inorganic hybrization.In vitro cell culture tests reveal that,compared with pure HA and pure Ti,the HA/collagen composite coating exhibit a best biological properties.

A Computational Chemistry Study Of Spin Traps., Jacob Fosso-Tande

Electronic Theses and Dissertations

Many defects in physiological processes are due to free radical damage: reactive oxygen species, nitric oxide, and hydroxyl radicals have been implicated in the parthenogenesis of cancer, diabetes mellitus, and rheumatoid arthritis. We herein characterize the phenyl-N-ter-butyl nitrone (PBN) type spin traps in conjunction with the most studied dimethyl-1-pyrroline-N-oxide (DMPO) type spin traps using the hydroxyl radical. In this study, theoretical calculations are carried out on the two main types of spin traps (DMPO and PBN) at the density functional theory level (DFT). The energies of the optimized structures, hyperfine calculations in gaseous and aqueous phases of the spin traps …

The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon

Chemistry Faculty Publications

The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the “blunt-end” of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive π-electron surface …

Mixed Quantum-Classical Molecular Dynamics Study Of A Hydrated Electron And An Investigation Of Temperature Control Algorithms, Janet Aremu-Cole

All Dissertations

The use of classical and quantum mechanics has been employed in this dissertation to study temperature control algorithms and a hydrated electron. A comparison of the effects of four commonly used temperature control algorithms on the energetics and dynamics of liquid water has been executed, in efforts to better understand the non-equipartitioning effects caused by some thermostats. The Berendsen, Andersen, Langevin, and velocity rescaling temperature control algorithms were applied to both dimer and bulk water systems, using the TIP4P water model. The two deterministic thermostats, Berendsen and velocity rescaling, display the 'flying ice cube effect' that had been noticed earlier …

Compartmentalization Of Hiv-1 In The Secondary Lymphoid Tissues, James Peter Gregson

Theses and Dissertations

Follicular dendritic cells (FDCs) reside in the lymphoid follicles of the secondary lymphoid tissues (sLTs). Following the infection of an individual with human immunodeficiency virus type 1 (HIV-1), viral particles are trapped in massive quantities on the surfaces of FDCs. HIV-1 viral compartments are cell types or tissues between which there is a restriction of virus flow. Compartmentalization of HIV-1 creates numerous sites within the body in which the virus can undergo independent evolution, giving rise to a more diverse total viral population. Given the sessile nature of the FDC, I hypothesized that contrary to common assumptions, FDC-trapped HIV-1 is …

Metal-Mediated Peptide Assembly: Use Of Metal Coordination To Change The Oligomerization State Of An Α-Helical Coiled-Coil, Mikhail V. Tsurkan, Michael Y. Ogawa

Chemistry Faculty Publications

Metal coordination is used to alter the oligomerization state of a designed peptide structure. The 30-residue polypeptide AQ-Pal21 4Pal21 contains two metal-binding 4-pyridylalanine (Pal) residues on its solvent-exposed surface and exists as a very stable two-stranded a-helical coiled-coil. Upon the addition of Pt(en)(NO3)(2), a significant conformational change to a metal-bridged, four-helix bundle is seen.

Department Of Chemistry News For Alumni And Friends, August 2007, Illinois State University, Department Of Chemistry

Chem Letter

Newsletter of the Illinois State University Department of Chemistry

Synthesis And Characterization Of Doped Core/Shell Quantum Dots, Elizabeth J. Sodt

Masters Theses

The central theme of the research performed is the systematic modification of the optical properties of quantum dots by the formation of a shell of another quantum dot of a different band gap energy. Core/shell quantum dots such as CdS:Mn/CdS, CdS:Mn/ZnS, and ZnS:Mn/CdS with various concentrations of dopant Mn²⁺ in the core and shell concentrations have been synthesized under mild conditions in the aqueous phase using stoichiometric amounts of the surfactant stabilizer dodecyl sulfate. These quantum dots exhibit UV-vis, emission, and electron paramagnetic resonance (EPR) spectral behavior that is dependent on the concentration of the shell and the dopant …

Fluorescent Photoinduced Electron Transfer (Pet) Proton Sensors, Risper Nyabeta

Theses, Dissertations and Culminating Projects

Two new fluorescent photoinduced electron transfer (PET) proton sensors based on anthracene and pyrazoline chromophores have been prepared. The anthracene sensor was prepared through alkylation of 2-pyridylcarbinol with 9-chloromethylanthracene and the pyrazoline sensor was prepared through an aldol condensation of 4- carboxybenzaldehyde and acetylpyridine followed by reaction with phenylhydrazine. The fluorescence of these sensors is modulated by the initiation or quenching of a PET process between the chromophore and a receptor due to protonation. The synthesis, characterization and proton binding studies of the new sensors are reported in this thesis.