Digital Commons Network^™

Role Of Structural Dynamics In Selectivity And Mechanism Of Non-Heme Fe(Ii) And 2-Oxoglutarate-Dependent Oxygenases Involved In Dna Repair, Sodiq Waheed, Rajeev Ramanan, Shobhit Chaturvedi, Nicolai Lehnert, Christopher J. Schofield, Christo Z. Christov, Tatyana Karabencheva-Christova

Michigan Tech Publications, Part 1

AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m₃C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a …

Discovery Of A Dna-Binding Consensus And Potential Genomic Regulatory Binding Sites For The Thermus Thermophilus Hb8 Transcriptional Regulator Ttha1359, Josiah Teague

Master of Science in Chemical Sciences Theses

Transcription factor (TF) proteins act as molecular mechanisms that modulate the initiation of the first step in the expression of genes, gene transcription. Currently, knowledge of the DNA-binding specificities and genes regulated by many TFs, including those of well-studied model organisms such as Escherichia coli and Thermus thermophilus, remains incomplete or lacking which renders gaps in the understanding of the regulatory networks and systems biology of many organisms. Cyclic-AMP receptor protein (CRP) regulators and fumarate and nitrate reduction regulator (FNR) proteins compose the CRP/FNR superfamily of TFs, a diverse subgroup of TFs in bacteria which regulate various gene expression programs. …

Antibacterial Properties Of Novel Amphiphiles, Ariana Simeone

Masters Theses, 2020-current

Hospital acquired infections, particularly antibiotic resistant infections, are a growing concern due to their infection and mortality rate, as well as their growing economic burden, and it has been estimated that by the year 2050 the associated mortality rate will be around 10 million deaths per year. A solution to this is better means of prevention, and amphiphiles, compounds with at least one hydrophilic head group and at least one hydrophobic tail, are promising candidates for stopping the spread of infectious bacteria. Novel amphiphiles with two bipyridinium head groups, separated by a hydrophobic carbon spacer of varying lengths, and each …

Raman Spectroscopy Study Of Delta-9-Tetrahydrocannabinol And Cannabidiol And Their Hydrogen-Bonding Activities, Kalee Sigworth

Honors Theses

Cannabis and products containing its cannabinoids have grown rapidly in acceptance and use in recent years with legalization of cannabis in many countries and US states. Cannabidiol and Delta-9-Tetrahydrocannabinol are two primary cannabinoids in Cannabis that have been shown to produce analgesic effects along with many other positive side effects for the user. These two cannabinoids interact with receptors in the Central and Peripheral Nervous Systems. No spectroscopic study to our knowledge has been performed to analyze the hydrogen bonding effects of interactions between these two cannabinoids and solvents. Here, we employ theoretical Raman spectra through computational methods to study …

Mineral-Surface Chemistry Of Hydroxyapatite And Urea-Rich Solutions, Estefania Garcia

Master of Science in Chemical Sciences Theses

On this planet the development of life requires six essential elements: C, H, O, N, P, and S. These elements are present in gaseous form, with the exception of phosphorus, which is primarily found in solid mineral sources. Phosphorus in biological systems is significant through its involvement in metabolic functions (e.g., Coenzyme A), cell structure (i.e., phospholipid membranes), and genetic storage/transfer (i.e., phosphodiester bonds in DNA and RNA). However, an ambiguity remains with the assimilation of phosphorus in biological systems, caused by its habitual presence in insoluble phosphate mineral sources. Recent research has found that insoluble phosphate …

Using A Novel Cell- Penetrating Peptide Technology To Induce Pluripotency, Laura-Maria Oja

Master of Science in Chemical Sciences Theses

Somatic stem cells have been used as a regenerative medicine tool to treat diseases like leukemia for decades, but they are limited in their ability to self-renew and differentiate. A better alternative, induced pluripotent stem cells (iPSCs), has the ability to generate cells from all three germ layers and avoid tissue rejection as well as bypass the ethical concerns related to embryonic stem cells. In 2006, Takahashi and Yamanaka discovered that only four genes were required to induce pluripotency: Oct4, Sox2, Klf4, and c-Myc (OSKM). Since then, pluripotency has been induced with OSKM most effectively by transfection or transduction. However, …

Huisgen 1,3-Dipolar Azide-Alkyne Cycloaddition “Click” Reaction In Polymer Synthesis And Curing, Jie Wu

Dissertations

This dissertation’s key focus is on utilizing Huisgen 1,3-dipolar azide-alkyne cycloaddition (AAC) reaction in copolymer synthesis and modification, including thermoplastic block copolymer and commercially available two-component polyurethane system. It can be divided into two major projects, introduced as follows.

The first project involves the development of a modular synthetic approach toward polyisobutylene (PIB)-based triphasic pentablock thermoplastic elastomer with enhanced moisture permeability. This terpolymer consists of a poly(styrene-b-isobutylene-b-styrene) (SIBS) core and appended hydrophilic polymer blocks (HBs). The SIBS core was synthesized via living cationic polymerization (LCP) of isobutylene followed by sequential addition of styrene. AAC was utilized …

Temperature Dependence On Enzymatic Activity Of A82f F87a Mutant And Wild-Type Cytochrome P450 Bm-3, Sally Seder

Undergraduate Theses

Cytochrome P450 is an enzyme mainly found in liver cells. It plays a key role in the breakdown of drugs and toxins by hydroxylating substrates making the substrates more water soluble. P450s are also involved in cholesterol and hormone synthesis. The third P450 from bacterium Bacillus Megaterium (BM3) is used as a model P450 enzyme due to its structural similarity to human P450s and due to its efficiency in the hydroxylation of fatty acids. Within the enzyme’s active site, substrates can occupy a distal or proximal conformation monitored by UV-vis spectroscopy. The proximal conformation is more effective when it comes …

Effect Of Quinoline Amide Substituents On The Luminescence And Magnetic Resonance Imaging (Mri) Properties Of Bimodal Europium (Iii) Complexes, Brooke Aloe, Marisa Poveda

Creative Activity and Research Day - CARD

Surgical intervention is often necessary in the management of cancer; however, sufficient tumor resection is reliant on adequate discrimination between malignant and healthy tissues. A dual-modality imaging agent with Magnetic Resonance Imaging (MRI) and Optical Imaging capabilities has the potential to improve tumor visualization before and during surgery. Administration of the agent would provide preoperative MR images that localize the bulk of the tumor and intraoperative fluorescence imaging would elucidate tumor margins. Macrocyclic lanthanide complexes possess long-lived luminescent lifetimes, making them ideal candidates for this class of imaging probe; however, the use of high energy lasers to directly excite these …

Oxidation Of Alpha-Pinene Initiated By O(3p) And Analyze Via Synchrotron Radiation, Ryan Rodriguez

Creative Activity and Research Day - CARD

Alpha-pinene oxidation is initiated via photolytically generated atomic oxygen O(3P). Reactions were analyzed at 550 K under 4 torr and 750 K at 5 torr. Reaction products are analyzed using multiplexed photoionization mass spectrometry. Vacuum ultraviolet synchrotron radiation is generated at the Advanced Light Source at the Lawrence Berkeley National Laboratory. Kinetic time traces are used to identify primary products, which are then characterized by comparing the experimental photoionization spectra to literature and/or simulated spectra. Calculations using the CBS-QB3 composite method suggest oxygen addition is the favorable pathway vs hydrogen abstraction, agreeing with experimental data. Branching fractions have determined for …

A Ficellomycin Inspired Platform: Modulating Cytotoxicity By Tuning The Instability Of Substituted Azabicyclo[3.1.0]Hexanes, Nathaniel Garrison

Creative Activity and Research Day - CARD

DNA-damaging natural products, despite their promising activity, are often too toxic for clinical use as anti-cancer chemotherapies. Novel strategies to effectively modulate their cytotoxicity could expand the arsenal of usable drugs. Ficellomycin, a cytotoxic, DNA-alkylating antibiotic with a rare and unstable azabicyclo[3.1.0]hexane core, undergoes an intramolecular cyclization to render itself inert outside of a narrow pH range. Exploration of ficellomycin’s natural capacity for self-regulation may present a novel strategy for modulation of cytotoxicity more generally. Toward this end, we have synthesized a protected ficellomycin precursor in four steps and 6% overall yield. Key steps in the sequence include Sharpless asymmetric …

Functional Nanomaterials By Combining Aminooxy Chemistry And Iodine Activation At Momolayer Protected Clusters., Tirtha Raj Sibakoti

Electronic Theses and Dissertations

Aminooxy (-ONH₂) groups are most commonly known for their chemoselective reaction with carbonyl compounds (aldehydes/ketones) under mild reaction conditions. Aminooxy-based click chemistry is a versatile means of ligation as evidenced by broad application in material science, biology, biochemistry, analytical chemistry, and nanoscience. Our work exploits the facile reaction of aminooxy groups presented on the surface of gold (Au) or palladium (Pd) monolayer protected clusters (MPCs) with various aldehydes via oximation reactions, which form the robust oxime ether adducts. The functionalization of hexanethiolate-stabilized Au MPCs with a newly developed trifunctional amine-containing aminooxy alkanethiol ligand by thiol place-exchange affords aminooxylated …

Nano-Scintillators As Next Generation Tools For Optogenetics, Ashley Dickey

All Dissertations

Optogenetics is a technique that is used to study neural pathways and has the ability to activate or silence synaptic behavior using visible light. Currently, the visible light sources used for optogenetics are surgically implanted into the brain tissue, but this harmful and invasive technique may be avoided if suitable scintillating nanoparticles can be inserted via injection. The proposed nano-scintillator particles must adhere to rigorous parameters including being under 100 nm, uniform, nontoxic, and dispersible to be successful in this biological system. The phase, crystallinity, and dopant concentration must be optimized to absorb X-ray radiation and emit photons of the …

Synthesis And Characterization Of Carbon Monoxide Producers Bipyridine Flavonolate Palladium(Ii) And Platinum(Ii) Complexes: Potential Anti-Cancer Agents, Sarah Whitfield

Electronic Theses and Dissertations

Novel designed metal ligand complexes as prodrugs are useful in the effort to find more effective and selective anti-cancer treatments. Carbon monoxide, CO, is known to induce mitochondrial collapse in cancer cells. Herein is described the synthesis of seven novel bipyridine flavonolate palladium(II) and platinum(II) complexes with the property of releasing carbon monoxide, and their characterization with FTIR, UV-Vis, fluorescence, NMR, and ESI mass spectra. Their ability to release carbon monoxide was investigated through oxygenation reaction under various conditions of temperature and light irradiation. The nitroxygenation reaction of the palladium complexes was also studied with nitrosyl hydride, HNO, generated in …

Discovery Of Single-Stranded Dna Aptamers For The Detection Of Ranavirus, Allyssa Angel

Theses, Dissertations and Culminating Projects

A key problem when developing molecular diagnostic techniques is procuring target detection probes. The need of a stable and selective probe is necessary for accurate target identification in disease detection. Antibodies are widely used but they are unstable at ambient temperatures and are expensive and time consuming to develop. The use of aptamers (short singlestranded DNA) as molecular probes provides several advantages over protein-based methods because they are more stable, easily selected and modifiable. The need of a reliable and stable probe is necessary for accurate detection tests in the field for disease monitoring. Currently, field methods are limited in …

Determining Donor Age Through Blood Analysis Using Attenuated Total Reflection Fourier Transform-Infrared (Atr Ft-Ir) Spectroscopy For Forensic Purposes, Samantha Leigh Giuliano

Legacy Theses & Dissertations (2009 - 2024)

Chapter 1 of this thesis is an overview of the use of attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy in industry and for examination of body fluids with emphasizes on examination of blood. It covers recent developments for analysis of samples with ATR FT-IR spectroscopy for forensic purposes.

Enhancing Upconversion Nanoparticle Performance Of Nayf4: Yb,Tm With Doping Optimization And Shell Addition And Of Nayf4: Yb,Er With Yb,Nd Shell Addition, Ashleigh M. Chov

Honors Thesis

Upconversion (UC), is a phenomenon that occurs when low-energy excitation (usually near-infrared (NIR)) results in higher-energy emission. Upconversion nanoparticles (UCNPs) are particles less than 100 nm in size that are synthesized using rare earth metals such as Yb, Er, Tm, and Y. UCNPs have important applications in a variety of fields, including bio-imaging, security printing, and latent fingerprint development. Traditional methods for latent fingerprint development such as fluorescent powder dusting have several drawbacks including low contrast, high background interference, and autofluorescence. NIR-to-NIR UCNPs are composed of NaYF₄: Yb, Tm and emit 800 nm light under 980 nm excitation …

Discriminating Azo Dyes: Conjugated Polymers, The Inner Filter Effect, And Array Sensors, Erin Crater

Honors Theses

Azo dyes are abundant pollutants that contaminate water supplies and threaten humans, biota, and ecosystem health. Their detection and discrimination are an incredible challenge due to the structural, chemical, and optical similarities between dyes, the complexity of the wastewater environment in which they are found, and their low environmental concentrations. In this work, the inner filter effect (IFE), combined with conjugated polymer array-based sensing, is utilized for the quantitative profiling of these pollutants. The array was constructed using three fluorescent, anionic conjugated polyelectrolytes whose varying spectroscopic properties led to distinct IFE patterns in the presence of the dyes. The unique …

Thiol-Ene Click Chemistry For Solid State Triplet-Triplet Annihilation Upconversion And Parts-Per-Billion Pyrophosphate Sensing In Artificial Seawater, Abagail K. Williams

Master's Theses

Thiol-ene click chemistry is a robust approach to molecularly engineering polymers for many applications. Within this work, thiol-ene click chemistry is used to fabricate thiol-ene networks for TTA-UC and to synthesize a conjugated polyelectrolyte (CPE) used as a pyrophosphate (PPi) sensor in complex aqueous media. Chapter I focuses on the synthesis and upconversion performance of rubbery networks fabricated using thiol-ene click photopolymerization. The advancement of triplet-triplet annihilation based upconversion (TTA-UC) in emerging technologies necessitates the development of solid-state systems that are readily accessible and broadly applicable. We demonstrate that thiol-ene click chemistry can be used as a facile cure-on-demand synthetic …

Electrochemical Reduction Of Carbon Dioxide And Carbon Monoxide For The Production Of Green Fuels And Chemicals., Jacob M. Strain

Electronic Theses and Dissertations

It has become apparent that closing the carbon cycle on this planet in order to mitigate disastrous consequences of runaway global warming has become one of the most pressing issues of our civilization. One of the ways we need to accomplish this goal is by finding news methods to generate fuels that will be carbon neutral. Renewable fuels and green chemicals will be a major component of closing the carbon cycle and restoring our planet’s ecosystem into a sense of balance. A method that can help achieve this goal is the reduction of CO₂. If CO₂ can …

Computational Modeling Of Photolysis And Catalysis Reactions In Vitamin B12-Dependent Enzymes., Abdullah Al Mamun

Electronic Theses and Dissertations

Vitamin B₁₂ is a complex organometallic molecule, the derivatives of which such as adenosylcobalamin (AdoCbl) and methylcobalamin (CH₃Cbl) act as a cofactor in numerous enzymatic reactions. These two biologically active cofactors contain a unique organometallic Co-C σ bond. Important feature of this Co-C bond is that it can be activated by both thermally and photolytically inside the enzymatic environment as well as in the solution. In the case of enzymatic reactions where AdoCbl molecule act as a cofactor, the cleavage of the Co-C bond constitutes the key catalytic step. The most intriguing features of this cleavage is …

Size-Dependent Inhibitory Effects Of Antibiotic Nanocarriers On Filamentation Of E. Coli, Preeyaporn Songkiatisak, Feng Ding, Pavan Kumar Cherukuri, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Multidrug membrane transporters exist in both prokaryotic and eukaryotic cells and cause multidrug resistance (MDR), which results in an urgent need for new and more effective therapeutic agents. In this study, we used three different sized antibiotic nanocarriers to study their mode of action and their size-dependent inhibitory effects against Escherichia coli (E. coli). Antibiotic nanocarriers (AgMUNH–Oflx NPs) with 8.6 × 10², 9.4 × 10³ and 6.5 × 10⁵ Oflx molecules per nanoparticle (NP) were prepared by functionalizing Ag NPs (2.4 ± 0.7, 13.0 ± 3.1 and 92.6 ± 4.4 nm) with a monolayer …

Optimizing The Synthesis Of A Theranostic Rhodamine, Alessandra Maisielou Rivera, Jonathan Alexander, Nathaniel Garrison

Creative Activity and Research Day - CARD

Current designs for small molecule theranostics, which serve both a diagnostic and therapeutic role, often involve dyes linked to therapeutic agents through a cleavable, traceless linker. In order to facilitate the separation of the dye from the therapeutic in response to a biological or chemical stimulus, linkers must incorporate elements of molecular logic, increasing their complexity and the overall bulk of the small molecule theranostic. By combining the self-immolative molecular logic of the linker into the structure of the dye itself, we hope to create a series of smaller, more atom-economical theranostics. Rhodamine dyes, which naturally possess aromatic rings with …

Development Of Hyperpolarizable Macrocyclic 13c-Probes For The Quantification Of Metals In Vivo, Holly Clancy

Creative Activity and Research Day - CARD

Numerous studies have shown correlations between various diseases, such as cancer and Alzheimer’s disease, and a change in the concentration of metals in tissues. Current blood analysis-based methods of metal quantification do not always provide a sense of metal concentration in tissue samples. With this work, we aim to develop a non-surgical method to quantify metal concentrations in human tissue. Hexadentate ligands such as ethylenediaminetetraacetic acid (EDTA) tagged with a 13C label at the carbonyl position have shown specific shifting of the carbonyl peak upon complexation with various metals via magnetic resonance spectroscopy (MRS). Additionally, these compounds have shown increased …

Determining The Mechanical Properties Of The E. Coli Methionine Transporter, Kha Andy Tran

Creative Activity and Research Day - CARD

Adenosine Triphosphate Binding Cassette (ABC) transporters constitute a superfamily of active transporters embedded in the cellular membrane. They consist of two highly conserved nucleotide-binding subunits which bind and hydrolyze ATP, and two diverse transmembrane subunits which provide a pathway for the substrate to pass through the membrane. ABC transporters serve a broad range of vital functions. Various conditions like cystic fibrosis and Stargardt disease are caused by defunct ABC transporters, and certain medical complications like antibiotic drug resistance are linked to promiscuous ABC transporters. Despite the importance of these transporters in crucial biological processes, the mechanisms of many transporters are …

Towards The Development Of Redox-Responsive Eu(Iii) Complexes For Cancer Imaging, Matthew Derfus

Creative Activity and Research Day - CARD

Cancer cells display redox dysregulation and lowered cytosolic pH as a means to maintain their over-proliferation. The development of an approach to probe tissue redox state could potentially allow discrimination between healthy and cancerous tissues. Magnetic Resonance Imaging (MRI) is a non-invasive technique used in the diagnosis of a variety of pathologies. The high spatial resolution and its use of non-ionizing radiation make MRI an attractive technique for cancer screening and detection. The quality of an MR image can be further enhanced with the aid of contrast agents, the majority of which are Gd(III) complexes. Gd(III) complexes provide positive contrast …

Investigating The Mechanism Of The E.Coli Atp-Binding Cassette Transporter Metni, Matthew Foronda

Creative Activity and Research Day - CARD

Intracellular chemical homeostasis is vital for cell survival. A key component for the maintenance of this homeostasis is ABC (ATP-binding cassette) transporters. These highly-conserved transporters utilize the energy from ATP binding and hydrolysis to move a wide array of substrates against their chemical gradient. Mutations can lead to a variety of diseases including cystic fibrosis and drug-resistant tumors. In order to solve these issues, these transporters must be well-studied. This project focuses on the mechanism of the methionine importer MetNI in E. coli, a reliable model for many transporters. Using fluorescence anisotropy, the apo-form of the substrate-binding protein (SBP) was …

A Cascade Reaction Of Cinnamyl Azides With Acrylates Directly Generates Tetrahydro-Pyrrolo-Pyrazole Heterocycles, Angela S. Carlson, En Chih Liu, Joseph J. Topczewski

Chemistry Faculty Research & Creative Works

Developing reactions to generate complex and modular building blocks in a concise and direct fashion remains a contemporary synthetic challenge. This work describes a stereoselective cascade reaction between allylic azides and acrylates that directly generates tetrahydro-pyrrolo-pyrazole ring systems. These products contain up to four contiguous stereocenters, two of which may be tetrasubstituted carbon atoms attached to a nitrogen atom. Over 30 examples are provided with an average isolated yield of 71% (ranging from 40% to 94%). The reaction was easily scaled to use more than one gram of starting material, and the products can be readily diversified.

Improving Biodiesel Through Pyrolysis: Direct Dynamics Investigations Into Thermal Decomposition Of Methyl Linoleate, Michael Bakker

Graduate Theses/Dissertations

Dependence on petroleum and petrochemical products is unsustainable as it is both a finite resource and environmentally hazardous. Biodiesel is a proposed alternative, but has complications including possessing poor cold weather operability and lacking the ability to supplement other petrochemical products (e.g., ethylene, hexane, etc.) relied upon in society. Pyrolysis of biodiesel has demonstrated the formation of smaller hydrocarbons comprising many of these petrochemical products. Our aim is to computationally simulate the pyrolysis of methyl linoleate, the most prevalent component in biodiesel formed in the US (from soybean). We make use of unimolecular direct dynamics describing intramolecular processes, introducing Temperature …

Probing Nanoelectroporation And Resealing Of The Cell Membrane By The Entry Of Ca2+ And Ba2+ Ions, Wenfei Bo, Mantas Silkunas, Uma Mangalanathan, Vitalij Novickij, Maura Casciola, Iurii Semenov, Shu Xiao, Olga N. Pakhomova, Andrei G. Pakhomov

Bioelectrics Publications

The principal bioeffect of the nanosecond pulsed electric field (nsPEF) is a lasting cell membrane permeabilization, which is often attributed to the formation of nanometer-sized pores. Such pores may be too small for detection by the uptake of fluorescent dyes. We tested if Ca²⁺, Cd²⁺, Zn²⁺, and Ba²⁺ ions can be used as nanoporation markers. Time-lapse imaging was performed in CHO, BPAE, and HEK cells loaded with Fluo-4, Calbryte, or Fluo-8 dyes. Ca²⁺ and Ba²⁺ did not change fluorescence in intact cells, whereas their entry after nsPEF increased fluorescence within <1 ms. The threshold for one 300-ns pulse was at 1.5–2 kV/cm, much lower than >7 …