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Description
There is a critical need for the development of clean and efficient energy sources. Hydrogen is being explored as a viable alternative to fuels in current use, many of which have limited availability and detrimental byproducts. Biological photo-production of H2 could provide a potential energy source directly manufactured from water and sunlight. As a part of the photosynthetic electron transport chain (PETC) of the green algae Chlamydomonas reinhardtii, water is split via Photosystem II (PSII) and the electrons flow through a series of electron transfer cofactors in cytochrome b6f, plastocyanin and Photosystem I (PSI). The terminal electron acceptor of PSI is ferredoxin, from which electrons may be used to reduce NADP+ for metabolic purposes. Concomitant production of a H+ gradient allows production of energy for the cell. Under certain conditions and using the endogenous hydrogenase, excess protons and electrons from ferredoxin may be converted to molecular hydrogen. In this work it is demonstrated both that certain mutations near the quinone electron transfer cofactor in PSI can speed up electron transfer through the PETC, and also that a native [FeFe]-hydrogenase can be expressed in the C. reinhardtii chloroplast. Taken together, these research findings form the foundation for the design of a PSI-hydrogenase fusion for the direct and continuous photo-production of hydrogen in vivo.
ContributorsReifschneider, Kiera (Author) / Redding, Kevin (Thesis advisor) / Fromme, Petra (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2013
Description
Telomerase is a unique reverse transcriptase that has evolved specifically to extend the single stranded DNA at the 3' ends of chromosomes. To achieve this, telomerase uses a small section of its integral RNA subunit (TR) to reiteratively copy a short, canonically 6-nt, sequence repeatedly in a processive manner using a complex and currently poorly understood mechanism of template translocation to stop nucleotide addition, regenerate its template, and then synthesize a new repeat. In this study, several novel interactions between the telomerase protein and RNA components along with the DNA substrate are identified and characterized which come together to allow active telomerase repeat addition. First, this study shows that the sequence of the RNA/DNA duplex holds a unique, single nucleotide signal which pauses DNA synthesis at the end of the canonical template sequence. Further characterization of this sequence dependent pause signal reveals that the template sequence alone can produce telomerase products with the characteristic 6-nt pattern, but also works cooperatively with another RNA structural element for proper template boundary definition. Finally, mutational analysis is used on several regions of the protein and RNA components of telomerase to identify crucial determinates of telomerase assembly and processive repeat synthesis. Together, these results shed new light on how telomerase coordinates its complex catalytic cycle.
ContributorsBrown, Andrew F (Author) / Chen, Julian J. L. (Thesis advisor) / Jones, Anne (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
The communication of genetic material with biomolecules has been a major interest in cancer biology research for decades. Among its different levels of involvement, DNA is known to be a target of several antitumor agents. Additionally, tissue specific interaction between macromolecules such as proteins and structurally important regions of DNA has been reported to define the onset of certain types of cancers.
Illustrated in Chapter 1 is the general history of research on the interaction of DNA and anticancer drugs, most importantly different congener of bleomycin (BLM). Additionally, several synthetic analogues of bleomycin, including the structural components and functionalities, are discussed.
Chapter 2 describes a new approach to study the double-strand DNA lesion caused by antitumor drug bleomycin. The hairpin DNA library used in this study displays numerous cleavage sites demonstrating the versatility of bleomycin interaction with DNA. Interestingly, some of those cleavage sites suggest a novel mechanism of bleomycin interaction, which has not been reported before.
Cytidine methylation has generally been found to decrease site-specific cleavage of DNA by BLM, possibly due to structural change and subsequent reduced bleomycin-mediated recognition of DNA. As illustrated in Chapter 3, three hairpin DNAs known to be strongly bound by bleomycin, and their methylated counterparts, were used to study the dynamics of bleomycin-induced degradation of DNAs in cancer cells. Interestingly, cytidine methylation on one of the DNAs has also shown a major shift in the intensity of bleomycin induced double-strand DNA cleavage pattern, which is known to be a more potent form of bleomycin induced cleavages.
DNA secondary structures are known to play important roles in gene regulation. Chapter 4 demonstrates a structural change of the BCL2 promoter element as a result of its dynamic interaction with the individual domains of hnRNP LL, which is essential to facilitate the transcription of BCL2. Furthermore, an in vitro protein synthesis technique has been employed to study the dynamic interaction between protein domains and the i-motif DNA within the promoter element. Several constructs were made involving replacement of a single amino acid with a fluorescent analogue, and these were used to study FRET between domain 1 and the i-motif, the later of which harbored a fluorescent acceptor nucleotide analogue.
Illustrated in Chapter 1 is the general history of research on the interaction of DNA and anticancer drugs, most importantly different congener of bleomycin (BLM). Additionally, several synthetic analogues of bleomycin, including the structural components and functionalities, are discussed.
Chapter 2 describes a new approach to study the double-strand DNA lesion caused by antitumor drug bleomycin. The hairpin DNA library used in this study displays numerous cleavage sites demonstrating the versatility of bleomycin interaction with DNA. Interestingly, some of those cleavage sites suggest a novel mechanism of bleomycin interaction, which has not been reported before.
Cytidine methylation has generally been found to decrease site-specific cleavage of DNA by BLM, possibly due to structural change and subsequent reduced bleomycin-mediated recognition of DNA. As illustrated in Chapter 3, three hairpin DNAs known to be strongly bound by bleomycin, and their methylated counterparts, were used to study the dynamics of bleomycin-induced degradation of DNAs in cancer cells. Interestingly, cytidine methylation on one of the DNAs has also shown a major shift in the intensity of bleomycin induced double-strand DNA cleavage pattern, which is known to be a more potent form of bleomycin induced cleavages.
DNA secondary structures are known to play important roles in gene regulation. Chapter 4 demonstrates a structural change of the BCL2 promoter element as a result of its dynamic interaction with the individual domains of hnRNP LL, which is essential to facilitate the transcription of BCL2. Furthermore, an in vitro protein synthesis technique has been employed to study the dynamic interaction between protein domains and the i-motif DNA within the promoter element. Several constructs were made involving replacement of a single amino acid with a fluorescent analogue, and these were used to study FRET between domain 1 and the i-motif, the later of which harbored a fluorescent acceptor nucleotide analogue.
ContributorsRoy, Basab (Author) / Hecht, Sidney M. (Thesis advisor) / Jones, Anne (Committee member) / Levitus, Marcia (Committee member) / Chaput, John (Committee member) / Arizona State University (Publisher)
Created2014
Description
Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified across all gold:silver ratios by a linear shift in the plasmon band maxima against alloy composition. The molar absorptivities of the NPs decreased non-linearly with increasing gold content from 2.0 x 108 M-1 cm-1 (fÉmax = 404 nm) for pure silver to 4.1 x 107 M-1 cm-1 (fÉmax = 511 nm) for pure gold. The NPs were immobilized onto transparent indium-tin oxide composite electrodes using layer-by-layer (LbL) deposition with poly(diallyldimethylammonium) acting as a cationic binder. The UV-Vis absorbance of the LbL film was used to calculate the surface coverage of alloy NPs on the electrode. Typical preparations had average NP surface coverages of 2.8 x 10-13 mol NPs/cm2 (~5% of cubic closest packing) with saturated films reaching ~20% of ccp for single-layer preparations (1.0 ~ 10-12 mol NPs/cm2). X-ray photoelectron spectroscopy confirmed the presence of alloy NPs in the LbL film and showed silver enrichment of the NP surfaces by ~9%. Irreversible oxidative dissolution (dealloying) of the less noble silver atoms from the NPs on LbL electrodes was performed by cyclic voltammetry (CV) in sulfuric acid. Alloy NPs with higher gold content required larger overpotentials for silver dealloying. Dealloying of the more-noble gold atoms from the alloy NPs was also achieved by CV in sodium chloride. The silver was oxidized first to cohesive silver chloride, and then gold dealloyed to soluble HAuCl4- at higher potentials. Silver oxidation was inhibited during the first oxidative scan, but subsequent cycles showed typical, reversible silver-to-silver chloride voltammetry. The potentials for both silver oxidation and gold dealloying also shifted to more oxidizing potentials with increasing gold content, and both processes converged for alloy NPs with >60% gold content. Charge-mediated electrochemistry of silver NPs immobilized in LbL films, using Fc(meOH) as the charge carrier, showed that 67% of the NPs were electrochemically inactive.
ContributorsStarr, Christopher A (Author) / Buttry, Daniel A (Thesis advisor) / Petuskey, William (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2014
Description
Hydrogenases catalyze the interconversion of protons, electrons, and hydrogen according to the reaction: 2H+ + 2e- <-> H2 while using only earth abundant metals, namely nickel and iron for catalysis. The enzymatic turnover of Clostridium acetobutylicum [FeFe]-hydrogenase has been investigated through the use of electrochemical and scanning probe techniques. Scanning tunneling microscopy (STM) imaging revealed sub-monolayer surface coverage. Cyclic voltammetry yielded a catalytic, cathodic hydrogen production signal similar to that observed for a platinum electrode. From the direct observation of single enzymes and the macroscopic electrochemical measurements obtained from the same electrode, the apparent turnover frequency (TOF) per single enzyme molecule as a function of potential was determined. The TOF at 0.7 V vs. Ag/AgCl for the four SAMs yielded a decay constant for electronic coupling (β) through the SAM of ~ 0.82 Å -1, in excellent agreement with published values for similar SAMs. One mechanism used by plants to protect against damage is called nonphotochemical quenching (NPQ). Triggered by low pH in the thylakoid lumen, NPQ leads to conversion of excess excitation energy in the antenna system to heat before it can initiate production of harmful chemical species by photosynthetic reaction centers. Here a synthetic hexad molecule that functionally mimics the role of the antenna in NPQ is described. When the hexad is dissolved in an organic solvent, five zinc porphyrin antenna moieties absorb light, exchange excitation energy, and ultimately decay by normal photophysical processes. However, when acid is added, a pH-sensitive dye moiety is converted to a form that rapidly quenches the first excited singlet states of all five porphyrins, converting the excitation energy to heat and rendering the porphyrins kinetically incompetent to perform useful photochemistry. Charge transport was also studied in single-molecule junctions formed with a 1,7-pyrrolidine-substituted 3,4,9,10-Perylenetetracarboxylic diimide (PTCDI) molecule. A reduction in the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals energy gap due to the electronic properties of the substituents is seen when compared to an unsubstituted-PTCDI. The small HOMO-LUMO energy gap allows for switching between electron- and hole-dominated charge transport with a gate voltage, thus demonstrating a single-molecule ambipolar field effect transistor.
ContributorsMadden, Christopher (Author) / Moore, Thomas A. (Thesis advisor) / Jones, Anne (Committee member) / Tao, Nongjian (Committee member) / Arizona State University (Publisher)
Created2012
Description
The heliobacterial reaction center (HbRC) is widely considered the simplest and most primitive photosynthetic reaction center (RC) still in existence. Despite the simplicity of the HbRC, many aspects of the electron transfer mechanism remain unknown or under debate. Improving our understanding of the structure and function of the HbRC is important in determining its role in the evolution of photosynthetic RCs. In this work, the function and properties of the iron-sulfur cluster FX and quinones of the HbRC were investigated, as these are the characteristic terminal electron acceptors used by Type-I and Type-II RCs, respectively. In Chapter 3, I develop a system to directly detect quinone double reduction activity using reverse-phase high pressure liquid chromatography (RP-HPLC), showing that Photosystem I (PSI) can reduce PQ to PQH2. In Chapter 4, I use RP-HPLC to characterize the HbRC, showing a surprisingly small antenna size and confirming the presence of menaquinone (MQ) in the isolated HbRC. The terminal electron acceptor FX was characterized spectroscopically and electrochemically in Chapter 5. I used three new systems to reduce FX in the HbRC, using EPR to confirm a S=3/2 ground-state for the reduced cluster. The midpoint potential of FX determined through thin film voltammetry was -372 mV, showing the cluster is much less reducing than previously expected. In Chapter 7, I show light-driven reduction of menaquinone in heliobacterial membrane samples using only mild chemical reductants. Finally, I discuss the evolutionary implications of these findings in Chapter 7.
ContributorsCowgill, John (Author) / Redding, Kevin (Thesis advisor) / Jones, Anne (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2012
Description
The honors thesis presented in this document describes an extension to an electrical engineering capstone project whose scope is to develop the receiver electronics for an RF interrogator. The RF interrogator functions by detecting the change in resonant frequency of (i.e, frequency of maximum backscatter from) a target resulting from an environmental input. The general idea of this honors project was to design three frequency selective surfaces that would act as surrogate backscattering or reflecting targets that each contains a distinct frequency response. Using 3-D electromagnetic simulation software, three surrogate targets exhibiting bandpass frequency responses at distinct frequencies were designed and presented in this thesis.
ContributorsSisk, Ryan Derek (Author) / Aberle, James (Thesis director) / Chakraborty, Partha (Committee member) / Electrical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The development of sustainable catalysts that exhibit exceptional activity has become a major goal of organometallic chemists. Considering their low cost and environmentally benign nature, the use of base metals in catalysis has recently been explored. This dissertation is focused on the development of manganese catalysts for organic transformations and inorganic polymerizations. Previous advances in Mn-based hydrosilylation and hydroboration catalysis are reviewed in Chapter 1 and set the stage for the experimental work described herein.In Chapter 2, the electronic structure of [(2,6-iPr2PhBDI)Mn(μ-H)]2 is explored. This compound was evaluated by density functional theory calculations, SQUID magnetometry and EPR spectroscopy at low temperature. Single crystal X-ray diffraction data was collected for related compounds that feature bridging X-type ligands. The data revealed how bridging ligands impact the Mayer bond order between the two Mn atoms and explained why [(2,6-iPr2PhBDI)Mn(μ-H)]2 is an active catalyst for organic transformations.
Chapter 3 spotlights the first study to systematically demonstrate commercial aminosilane CVD precursor synthesis by way of SiH4 and amine dehydrocoupling using [(2,6-iPr2PhBDI)Mn(μ-H)]2. In addition, the study provided an efficient and halogen-free preparation of highly cross-linked polycarbosilazanes under ambient conditions. Furthermore, exceptionally pure perhydropolysilazane was directly prepared from ammonia and silane at room temperature through dehydrogenative coupling. These are also the first reported examples of Mn-catalyzed Si–N dehydrocoupling.
This research was then extended to the Mn-catalyzed dehydrogenative coupling of NH3 and diamines to organic silanes. Organic polysilazanes and polycarbosilazanes were synthesized and the structures were characterized by NMR, FT-IR, and MALDI-TOF spectroscopy. The thermal properties and coating applications of the products were evaluated by TGA, DSC, X-ray powder diffraction, SEM and EDX. A turnover frequency (TOF) experiment using 0.01 mol% of [(2,6-iPr2PhBDI)Mn(μ-H)]2 revealed a maximum TOF of 300 s-1, which is the highest activity ever reported for this transformation.
The last chapter highlights the first examples of nitrile dihydroboration mediated by a manganese catalyst. Using 0.5 mol% of [(2,6-iPr2PhBDI)Mn(μ-H)]2, 14 nitriles were reduced with HBPin at 80 ℃ to afford N,N-diborylamines after 24 h. A mechanism was proposed based on the isolation of [(2,6-iPr2PhBDI)Mn(NCHPh)]2 as an intermediate and further substantiated by DFT.
ContributorsNguyen, Thu Thao (Author) / Trovitch, Ryan (Thesis advisor) / Jones, Anne (Committee member) / Ackerman, Laura (Committee member) / Arizona State University (Publisher)
Created2022
Description
The ability of magnetic resonance imaging (MRI) to image any part of the human body without the effects of harmful radiation such as in CAT and PET scans established MRI as a clinical mainstay for a variety of different ailments and maladies. Short wavelengths accompany the high frequencies present in high-field MRI, and are on the same scale as the human body at a static magnetic field strength of 3 T (128 MHz). As a result of these shorter wavelengths, standing wave effects are produced in the MR bore where the patient is located. These standing waves generate bright and dark spots in the resulting MR image, which correspond to irregular regions of high and low clarity. Coil loading is also an inevitable byproduct of subject positioning inside the bore, which decreases the signal that the region of interest (ROI) receives for the same input power. Several remedies have been proposed in the literature to remedy the standing wave effect, including the placement of high permittivity dielectric pads (HPDPs) near the ROI. Despite the success of HPDPs at smoothing out image brightness, these pads are traditionally bulky and take up a large spatial volume inside the already small MR bore. In recent years, artificial periodic structures known as metamaterials have been designed to exhibit specific electromagnetic effects when placed inside the bore. Although typically thinner than HPDPs, many metamaterials in the literature are rigid and cannot conform to the shape of the patient, and some are still too bulky for practical use in clinical settings. The well-known antenna engineering concept of fractalization, or the introduction of self-similar patterns, may be introduced to the metamaterial to display a specific resonance curve as well as increase the metamaterial’s intrinsic capacitance. Proposed in this paper is a flexible fractal-inspired metamaterial for application in 3 T MR head imaging. To demonstrate the advantages of this flexibility, two different metamaterial configurations are compared to determine which produces a higher localized signal-to-noise ratio (SNR) and average signal measured in the image: in the first configuration, the metamaterial is kept rigid underneath a human head phantom to represent metamaterials in the literature (single-sided placement); and in the second, the metamaterial is wrapped around the phantom to utilize its flexibility (double-sided placement). The double-sided metamaterial setup was found to produce an increase in normalized SNR of over 5% increase in five of six chosen ROIs when compared to no metamaterial use and showed a 10.14% increase in the total average signal compared to the single-sided configuration.
ContributorsSokol, Samantha (Author) / Sohn, Sung-Min (Thesis director) / Allee, David (Committee member) / Jones, Anne (Committee member) / Barrett, The Honors College (Contributor) / Electrical Engineering Program (Contributor)
Created2022-05
Description
In recent years, researchers have employed DNA and protein nanotechnology to develop nanomaterials for applications in the fields of regenerative medicine, gene therapeutic, and materials science. In the current state of research, developing a biomimetic approach to fabricate an extracellular matrix (ECM)-like material has faced key challenges. The difficulty arises due to achieving spatiotemporal complexity that rivals the native ECM. Attempts to replicate the ECM using hydrogels have been limited in their ability to recapitulate its structural and functional properties. Moreover, the biological activities of the ECM, such as cell adhesion, proliferation, and differentiation, are mediated by ECM proteins and their interactions with cells, making it difficult to reproduce these activities in vitro.Thus, the work presented in my dissertation represents efforts to develop DNA and protein-based materials that mimic the biological properties of the ECM. The research involves the design, synthesis, and characterization of nanomaterials that exhibit unique physical, chemical, and mechanical properties. Two specific aspects of the biomimetic system have been to include (1) a modular protein building block to change the bioactivity of the system and (2) to temporally control the self-assembly of the protein nanofiber using different coiled coil mechanisms. The protein nanofibers were characterized using atomic force microscopy, transmission electron microscopy, and super-resolution DNA Point Accumulation for Imaging in Nanoscale Topology. The domains chosen are the fibronectin domains, Fn-III10, Fn-III9-10, and Fn-III12-14, with bioactivity such as cell adhesion and growth factor binding.
To extend this approach, these cys-nanofibers have been embedded in a hyaluronic acid scaffold to enable bioactivity and fibrous morphologies. Nanofiber integration within the HA gel has been shown to promote tunable mechanical properties and architectures, in addition to promoting a temporal display of the protein nanofibers. The hydrogels were characterized using scanning electron microscopy, mechanical compression testing, and fluorescence microscopy. The findings in this dissertation highlight the promise of biomimetic DNA and protein nanomaterials as a versatile approach for developing next-generation materials with unprecedented properties and functions. These findings continue to push the boundaries of what is possible in nanotechnology, leading to new discoveries that will have a significant impact on society.
ContributorsBernal-Chanchavac, Julio (Author) / Stephanopoulos, Nicholas (Thesis advisor) / Jones, Anne (Committee member) / Mills, Jeremy (Committee member) / Arizona State University (Publisher)
Created2023