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Multicolor Conjugated Polymer Dots For Biological Fluorescence Imaging, Changfeng Wu, Barbara Bull, Craig Szymanski, Kenneth Christensen, Jason Mcneill

Publications

Highly fluorescent conjugated polymer dots were developed for demanding applications such as fluorescence imaging in live cells. These nanoparticles exhibit small particle diameters, extraordinary fluorescence brightness, and excellent photostability. Single particle fluorescence imaging and kinetic studies indicate much higher emission rates (∼10⁸ s⁻¹) and little or no blinking of the nanoparticles as compared to typical results for single dye molecules and quantum dots. Analysis of single particle photobleaching trajectories reveals excellent photostability—as many as 10⁹ or more photons emitted per nanoparticle prior to irreversible photobleaching. The superior figures of merit of these new fluorescent probes, together …

2d Regional Correlation Analysis Of Single-Molecule Time Trajectories, Xuefei Wang, H. Peter Lu

Chemistry Faculty Publications

We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anticorrelated, or noncorrelated; after which, a cross-correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis. We specifically discuss an application of this approach to analyze single-molecule fluorescence …

Defining Resonance Raman Spectral Responses To Substrate Binding By Cytochrome P450 From Pseudomonas Putida, Piotr J. Mak, Daniel Kaluka, Munyaradzi Edith Manyumwa, Haiqing Zhang, Tianjing Deng, James R. Kincaid

Chemistry Faculty Research and Publications

Resonance Raman spectra are reported for substrate-free and camphor-bound cytochrome P450cam and its isotopically labeled analogues that have been reconstituted with protoheme derivatives that bear -CD₃ groups at the 1, 3, 5, and 8-positions (d12-protoheme) or deuterated methine carbons (d4-protoheme). In agreement with previous studies of this and similar enzymes, substrate binding induces changes in the high frequency and low frequency spectral regions, with the most dramatic effect in the low frequency region being activation of a new mode near 367 cm⁻¹. This substrate-activated mode had been previously assigned as a second “propionate bending” mode (Chen et …

Halothiobacillus Neapolitanus Carboxysomes Sequester Heterologous And Chimeric Rubisco Species, Balaraj B. Menon, Zhicheng Dou, Sabine Heinhorst, Jessup M. Shively, Gordon C. Cannon

Faculty Publications

Background: The carboxysome is a bacterial microcompartment that consists of a polyhedral protein shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme that catalyzes the first step of CO(2) fixation via the Calvin-Benson-Bassham cycle. Methodology/Principal Findings: To analyze the role of RubisCO in carboxysome biogenesis in vivo we have created a series of Halothiobacillus neapolitanus RubisCO mutants. We identified the large subunit of the enzyme as an important determinant for its sequestration into alpha-carboxysomes and found that the carboxysomes of H. neapolitanus readily incorporate chimeric and heterologous RubisCO species. Intriguingly, a mutant lacking carboxysomal RubisCO assembles empty carboxysome shells of …

Ex Situ Variable Angle Spectroscopic Ellipsometry Studies On Chemical Vapor Deposited Boron-Doped Diamond Films: Layered Structure And Modeling Aspects, S. Gupta, A. Dudipala, O. A. Williams, K. Haenen, Eric W. Bohannan

Chemistry Faculty Research & Creative Works

We report the optical property measurements on boron-doped diamond (BDD) films which were synthesized by microwave plasma-assisted chemical vapor deposition technique on Si (100) using methane in high hydrogen dilution and trimethylboron as precursors with varying boron concentration such that [B] [C]gas =100, 500, 1000, 2000, 4000, and 6467 ppm. These BDD films were investigated using a rotating analyzer variable angle spectroscopic ellipsometry (SE) from the near IR to UV range (830-193 nm). by applying the conventional Bruggeman effective medium approximation and linear regression analyses to the raw SE data that is, [ψ (λi),Δ (λi)] and pseudodielectric function (〈 εr …

Simple Inhibitors Of Histone Deacetylase Activity That Combine Features Of Short-Chain Fatty Acid And Hydroxamic Acid Inhibitors, Jessica L. Tischler, Basel Abuaita, Sierra C. Cuthpert, Christopher Fage, Kristi Murphy, Andrew Saxe, Edward B. Furr, Jamie Hedrick, Jennifer Meyers, David Snare, Ali R. Zand

Chemistry & Biochemistry Publications

Butyric acid and trichostatin A (TSA) are anti-cancer compounds that cause the upregulation of genes involved in differentiation and cell cycle regulation by inhibiting histone deacetylase (HDAC) activity. In this study we have synthesized and evaluated compounds that combine the bioavailability of short-chain fatty acids, like butyric acid, with the bidentate binding ability of TSA. A series of analogs were made to examine the effects of chain length, simple aromatic cap groups, and substituted hydroxamates on the compounds' ability to inhibit rat-liver HDAC using a fluorometric assay. In keeping with previous structure-activity relationships, the most effective inhibitors consisted of longer …

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 PlainGreen Conference 2008; Dioszegi attends ACS Green Chemistry Summer School

Page 3 SDSU seeks CLS/Medical Tech accreditation; Pravecek named South Dakota’s ASCLS Member of the Year

Page 4 You awarded grant from Board of Regents; Recent Faculty Publications

Page 5 New Grad Students

Page 6 Native American traditional tea has health benefits; Natalie Garry is SDSU August Career Service Employee

Page 7 Henry A. Lardy Lecture; SDSU offers master’s degree in chemistry education; Grad students attend Green Chemistry and Engineering Conference

Page 8 New Shepard Hall Update

Phosphorylation Of P27kip1 Regulates Assembly And Activation Of Cyclin D1-Cdk4, Michelle D. Larrea, Jiyong Liang, Thiago G. Da Silva, Feng Hong, Shan H. Shao, Kathy Han, D. Dumont, Joyce M. Slingerland

Chemistry and Physics Faculty Articles

p27 mediates Cdk2 inhibition and is also found in cyclin D1-Cdk4 complexes. The present data support a role for p27 in the assembly of D-type cyclin-Cdk complexes and indicate that both cyclin D1-Cdk4-p27 assembly and kinase activation are regulated by p27 phosphorylation. Prior work showed that p27 can be phosphorylated by protein kinase B/Akt (PKB/Akt) at T157 and T198. Here we show that PKB activation and the appearance of p27pT157 and p27pT198 precede p27-cyclin D1-Cdk4 assembly in early G₁. PI3K/PKB inhibition rapidly reduced p27pT157 and p27pT198 and dissociated cellular p27-cyclin D1-Cdk4. Mutant p27 allele products lacking phosphorylation at …

Molecular-Orientation-Dependent Ac Stark Effect And Its Impact On Multiphoton Processes, Xi Chu

Chemistry and Biochemistry Faculty Publications

We study the dependence of the ac Stark shifts of electronic energies on the molecular orientation relative to the polarization direction of an incident intense laser field, using a three-dimensional non-Hermitian Floquet method and H(2)+ as a model system. Simultaneously, we also study the orientation-dependent high-order harmonic generation (HHG) and multiphoton ionization (MPI). We find that with the presence of near-one-photon resonance, the Stark effect strongly mixes electronic states of different symmetries to create quasienergy states (QESs). The orientation dependence of multiphoton processes, in which these QESs play an important role, becomes complex. Population transfer is better achieved with aligned …

Fluorescence Sensor Array For Metal Ion Detection Based On Various Coordination Chemistries: General Performance And Potential Application, Zhuo Wang, Manuel A. Palacios, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

A sensor array containing 9 cross-reactive sensing fluorescent elements with different affinity and selectivity to 10 metal cations (Ca2+, Mg2+, Cd2+, Hg2+, Co2+, Zn2+, Cu2+, Ni2+, Al3+, Ga3+) is described. The discriminatory capacity of the array was tested at different ranges of pH and at different cation concentrations using linear discriminant analysis (LDA). Qualitative identification of cations can be determined with over 96% of accuracy in a concentration range covering 3 orders of a magnitude (5-5000 mu M). Quantitative analysis can be achieved with over 90% accuracy in the concentration range between 10 and 5000 mu M. The array performance …

Resonance Raman Spectroscopic Studies Of Hydroperoxo Derivatives Of Cobalt-Substituted Myoglobin, Piotr J. Mak, James R. Kincaid

Chemistry Faculty Research and Publications

Recent progress in generating and stabilizing reactive heme protein enzymatic intermediates by cryoradiolytic reduction has prompted application of a range of spectroscopic approaches to effectively interrogate these species. The impressive potential of resonance Raman spectroscopy for characterizing such samples has been recently demonstrated in a number of studies of peroxo- and hydroperoxo-intermediates. While it is anticipated that this approach can be productively applied to the wide range of heme proteins whose reaction cycles naturally involve these peroxo- and hydroperoxo-intermediates, one limitation that sometimes arises is the lack of enhancement of the key intraligand ν(O–O) stretching mode in the native …

Synthetic Studies Directed Toward Amphidinol 2: Elucidation Of The Relative Configuration Of The C1–C10 Fragment, Praveen Kommana, Seung Won Chung, William A. Donaldson

Chemistry Faculty Research and Publications

Model compounds (11 and 12) for the C1–C10 tetrahydropyran fragment of amphidinol 2 were prepared from (2S)-benzyloxypropanal in 9 steps. The synthetic route relied on diastereoselective diene-aldehyde cycloaddition, stereoselective C-allylation, and reagent based enantioselective aldehyde allylation. Comparison of the NMR spectra for models 11 and 12 with that for amphidinol 2 indicated that the C1–C10 segment of the natural product possesses the 2R^*,4R^*,6R^*,7S^*,8R^*,10S^* relative configuration.

Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang

Faculty Publications

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

Reduction Of Toxicity In The Premature Neonate Addociated With Aluminum As A Contaminant Of Total Parenteral Nutrition Solution, Sujittra Srisung

Dissertations

Aluminum (Al) is the third most common element in the Earth?s crust. It is widely consumed in water, foods, and drugs. However, in humans, the uptake of aluminum into the body and its deposition in tissues has been linked to conditions of medical concern, including many neurological disorders such as dialysis dementia, Alzheimer?s disease, Parkinson?s dementia and Down?s syndrome. Premature neonates who receive intravenous feeding (TPN) are at a high risk for Al toxicity because the TPN solutions are contaminated with Al3+, which is not excreted effectively due to poor kidney development in these patients. The FDA has recommended regulations …

The Original Build Up Of Genetic Information By Rna Recombination, Eric John Hayden

Dissertations and Theses

This research demonstrates chemical reactions of RNA molecules that allow them to increase in length, from non-catalytic oligomers to complex RNA enzymes. The purpose of this research was to explain the origin of large RNA polymers required for life to begin in the proposed "RNA World". To do this, the Azoarcus group I ribozyme was engineered to catalyze phosphodiester exchange reactions that result in the recombination of short oligomer substrates marked by ^5'CAU^3' recognition tags.

To demonstrate the ability to produce catalytic RNA sequences through recombination, substrate oligomers were synthesized that could produce ribozymes if large portions of …

Iron Oxide Deposits Associated With The Ectosymbiotic Bacteria In The Hydrothermal Vent Shrimp Rimicaris Exoculata, Laure Corbari, Marie Anne Cambon-Bonavita, Gary J. Long, Fernande Grandjean, Magali Zbinden, Françoise Gaill, Philippe Compère

Chemistry Faculty Research & Creative Works

The Rimicaris exoculata shrimp is considered as a primary consumer that dominates the fauna of most Mid-Atlantic Ridge (MAR) hydrothermal ecosystems. These shrimps harbour in their gill chambers an important ectosymbiotic community of chemoautotrophic bacteria associated with iron oxide deposits. The structure and elemental composition of the mineral concretions associated with these bacteria have been investigated by using LM, ESEM, TEM STEM and EDX microanalyses. The nature of the iron oxides in shrimps obtained from the Rainbow vent field has also been determined by Mössbauer spectroscopy. This multidisciplinary approach has revealed that the three layers of mineral crust in the …

Linear Dichroism In Resonant Inelastic X-Ray Scattering To Molecular Spin-Orbit States, Renaud Guillemin, Stephane Carniato, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon

Chemistry and Biochemistry Faculty Research

Polarization-dependent resonant inelastic x-ray scattering (RIXS) is shown to be a new probe of molecular-field effects on the electronic structure of isolated molecules. A combined experimental and theoretical analysis explains the linear dichroism observed in Cl 2p RIXS following Cl 1s excitation in HCl and CF₃Cl as due to molecular-field effects, including singlet-triplet exchange, indicating polarized-RIXS provides a direct probe of spin-orbit-state populations applicable to any molecule.

Use Of Fluorinated Functionality In Enzyme Inhibitor Development: Mechanistic And Analytical Advantages, David B. Berkowitz, Kannan R. Karukurichi, Roberto De La Salud-Bea, David L. Nelson, Christopher D. Mccune

David Berkowitz Publications

On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the “bio-orthogonal” and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with ¹⁹Fmarkers, that then report back …

Non-Canonical Binding Of Calmodulin To Aquaporin-0: Implications For Channel Regulation, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homo-tetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show CaM binds the AQP0 C-terminal domain in a calcium dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a non-canonical fashion, suggesting a form of co-operativity between AQP0 monomers. Based on …

An Integrated Approach To The Toxicity Evaluation Of Irish Marine Sediment - Chemical Assessment, Michelle Giltrap

Doctoral

This project was a collaborative project between the Marine Institute (MI) in Galway and Radiation and Environmental Science Centre (RESC) in the Technological University Dublin (DIT). In Ireland, at present, sediment quality assessments are generally reliant on chemical analysis alone with limited bioassay techniques available to further characterise the sediment. Some causative agents of toxicity to biological organisms are below analytical detection limits. Integration of bioassay data with chemical analysis is essential in order to complete a full ecotoxicological assessment of the quality of the marine environment. This project describes the chemical analysis of marine sediment for persistent pollutants from …

2,9-Bis(1,3-Benzothia­Zol-2-Yl)-1,10-Phenanthroline Dichloro­Methane Disolvate, Jesmin Akther, Sergey V. Lindeman, Mohammad Rezaul Karim

Chemistry Faculty Research and Publications

In the title compound, C₂₆H₁₄N₄S₂·2CH₂Cl₂, the two pendant benzothia­zole groups are slightly twisted with respect to the phenanthroline core [dihedral angles = 1.03 (7) and 9.05 (5)°]. Weak inter­molecular C-HN and C-HCl inter­actions occur in the crystal structure.

Global Conformational Dynamics In Ras, Casey O'Connor, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

Ras and its homologues are central to regulation of a multitude of cellular processes. Ras in complex with GTP binds and activates its downstream signaling partners. ³¹P NMR studies indicated that the Ras−GTP conformation is heterogeneous on a millisecond time scale, but details of its conformational dynamics remain unknown. Here we present evidence that the conformational exchange process in human H-Ras complexed with GTP mimic GppNHp is global, encompassing most of the GTPase catalytic domain. The correlated character of conformational dynamics in Ras opens opportunities for understanding allosteric effects in Ras function.

Development Of Pharmacophore And Comfa Studies For Sigma2 Receptor Ligands, Laura Ann Wirpsza

Theses

This study describes the development of a pharmacophore and CoMIFA model for sigma 2 (σ₂) receptor ligands. CoMFA studies were performed for 32 bioactive σ₂ receptor ligands using the radioligand [H 3] (+) DTG in the presence of pentazocine. The pharmacophore was derived using Distance Comparisons (DISCOtech) from eight partially to highly active ~2 receptor ligands. All 32 compounds were calculated in three methods: AMi, HFI3~21G*, and B3LYP/3~21G* methods. These methods run in Gaussian 98 determined the geometry optimization and electrostatic charges for each molecule. CoMFA maps were developed using SYBYL ver. 7.2 to compare the electrostatic …

Inverse Velocity Dependence Of Vibrationally Promoted Electron Emission From A Metal Surface, N. H. Nahler, J. D. White, Jerry L. Larue, Daniel J. Auerbach, Alec M. Wodtke

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

All previous experimental and theoretical studies of molecular interactions at metal surfaces show that electronically nonadiabatic influences increase with molecular velocity. We report the observation of a nonadiabatic electronic effect that follows the opposite trend: The probability of electron emission from a low–work function surface—Au(111) capped by half a monolayer of Cs—increases as the velocity of the incident NO molecule decreases during collisions with highly vibrationally excited NO(X²π_½, V = 18; V is the vibrational quantum number of NO), reaching 0.1 at the lowest velocity studied. We show that these results are consistent with a vibrational …

New Functional Polymers For Alternative Energy Applications, Chulsung Bae

UNLV Renewable Energy Symposium

The 2008 UNLV Renewable Energy Symposium was presented by the Office of Strategic Energy Programs and co-sponsored by the Division of Research and Graduate Studies on August 20, 2008 on the UNLV campus.

The event focused on renewable energy production in Nevada, the US Southwest, and renewable research projects nationwide. It was a great opportunity for anyone working on renewable projects to collaborate with others in this field and exchange information. Over 230 individuals attended the event this year.

The Role Of Metal Coordnation In The Inhibition Of Iron(Ii)- And Copper(I)-Mediated Dna Damage By Organoselenium And Organosulfur Compounds, Erin Battin

All Dissertations

Copper and iron are two widely-studied transition metals associated with hydroxyl radical (OH) generation: Fe2+/Cu+ + H2O2 = Fe3+/Cu2+ + OH + OH-. Metal-mediated oxidative damage is a major cause of cellular DNA damage and death, and has been implicated in cancer, neurodegenerative, and cardiovascular diseases. Because sulfur and selenium antioxidants ameliorate oxidative damage, the ability of twenty biological sulfur- and selenium-containing compounds to inhibit metal-mediated DNA damage caused by hydroxyl radical has been quantified. In the Cu+/H2O2 system, six sulfur compounds and three selenium compounds inhibited DNA damage with IC50 values ranging from 3.3 to 25.5 μM. Several sulfur …

Effects Of Polyphenol Compounds On Iron-And Copper-Mediated Dna Damage: Mechanisms And Predictive Models, Nathan Perron

All Dissertations

Polyphenol compounds are widely recognized for their antioxidant activity; however, under some conditions these compounds can also exhibit prooxidant activity. This work examined the interactions of polyphenols with iron and copper to improve understanding of both their antioxidant and prooxidant effects. Polyphenols with catechol and gallol groups effectively inhibit iron-mediated oxidative DNA damage by chelating iron, with IC₅₀ values ranging from 1-59 µM. Gallate compounds are more potent than their catecholate analogues in every instance, and their antioxidant potencies correlate to pK_a values for the most acidic phenolic hydrogen. This correlation represents the first predictive model of …

Functionalized Carbon Nanotubes For Biological Applications, Lingrong Gu

All Dissertations

Carbon nanotubes with their unique pseudo-one-dimensional nanostructures and related electronic, optical, and mechanical properties have been attracting much attention for potential biological applications, such as biosensors, bio-delivery, bioimaging and so on. In this dissertation, recent studies and advances toward bioapplications of carbon nanotubes are critically reviewed, followed by detailed reports on my research projects concerning the use of carbon nanotubes as unique scaffolds for multivalent display of sugars and the relevant results from bio-evaluation of these novel nanomaterials.
Single-walled (SWNTs) and multiple-walled carbon nanotubes (MWNTs) were functionalized with amine-derivatived monosaccharides (galactoses and mannoses) and their dendritic constructs. These sugar-functionalized carbon …

Strategies For Expanding The Halogen Bonding Periodic Table And Desigining Complementary Halogen/Hydrogen Bonding Synthons, Hadi Arman

All Dissertations

Halogen bonding is the donation of electron density from an electron donor, such as N, O, S, Se atoms, to an electron acceptor such as a dihalogen or organohalogen. This interaction plays an important role in biological systems, such as the thyroid gland and is useful in many other fields such as drug design, crystal engineering, synthetic chemistry, material science and bioinorganic chemistry. However, currently there is a lack of information for this interaction in systems involving organoiodines with sulfur and selenium electron donors.
A variety of sulfur and selenium Lewis base donors were investigated with various organoiodines. The main …

Synthesis And Pharmacology Of N-Alkyl-3-(Halo-Naphthoyl)Indoles, Valerie Smith

All Dissertations

The medicinal values of marijuana have often been overshadowed due to the psychotropic, 'recreational' effects it brings about in a user. For hundreds of years the therapeutic uses of cannabis sativa were appreciated, but the inability to control the dosage of the main constituent, and therefore the psychotropic effects, rendered the drug a liability. The elucidation of the structure of this main psychoactive constituent, ∆9-tetrahydrocannabinol (∆9-THC) by Gaoni and Mechoulam in 1964 opened the door to the discovery of a vast array of knowledge about cannabinoids. From the multiple classes of cannabinoids and the ways these compounds interact with the …