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- Creators: Hayes, Mark
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Description
Rapid and reliable separation and analysis of proteins require powerful analytical methods. The analysis of proteins becomes especially challenging when only small sample volumes are available, concomitantly with low concentrations of proteins. Time critical situations pose additional challenges. Due to these challenges, conventional macro-scale separation techniques reach their limitations. While microfluidic devices require only pL-nL sample volumes, they offer several advantages such as speed, efficiency, and high throughput. This work elucidates the capability to manipulate proteins in a rapid and reliable manner with a novel migration technique, namely dielectrophoresis (DEP). Since protein analysis can often be achieved through a combination of orthogonal techniques, adding DEP as a gradient technique to the portfolio of protein manipulation methods can extend and improve combinatorial approaches. To this aim, microfluidic devices tailored with integrated insulating obstacles were fabricated to create inhomogeneous electric fields evoking insulator-based DEP (iDEP). A main focus of this work was the development of pre-concentration devices where topological micropost arrays are fabricated using standard photo- and soft lithographic techniques. With these devices, positive DEP-driven streaming of proteins was demonstrated for the first time using immunoglobulin G (IgG) and bovine serum albumin. Experimentally observed iDEP concentrations of both proteins were in excellent agreement with positive DEP concentration profiles obtained by numerical simulations. Moreover, the micropost iDEP devices were improved by introducing nano-constrictions with focused ion beam milling with which numerical simulations suggested enhancement of the DEP effect, leading to a 12-fold increase in concentration of IgG. Additionally, concentration of β-galactosidase was observed, which seems to occur due to an interplay of negative DEP, electroosmosis, electrokinesis, diffusion, and ion concentration polarization. A detailed study was performed to investigate factors influencing protein DEP under DC conditions, including electroosmosis, electrophoresis, and Joule heating. Specifically, temperature rise within the iDEP device due to Joule heating was measured experimentally with spatial and temporal resolution by employing the thermosensitive dye Rhodamine B. Unlike DNA and cells, protein DEP behavior is not well understood to date. Therefore, this detailed study of protein DEP provides novel information to eventually optimize this protein migration method for pre-concentration, separation, and fractionation.
ContributorsNakano, Asuka (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2014
Description
Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal of the tightly bound sugar phosphates from the active sites of RuBisCO. In this work, we investigated the ATP/ADP dependent oligomerization equilibrium of fluorescently tagged Rca for a wide range of concentrations using fluorescence correlation spectroscopy. Results show that in the presence of ADP-Mg2+, the oligomerization state of Rca gradually changes in steps of two subunits. The most probable association model supports the dissociation constants (K_d) of ∼4, 1, 1 μM for the monomer-dimer, dimer-tetramer, and tetramer-hexamer equlibria, respectively. Rca continues to assemble at higher concentrations which are indicative of the formation of aggregates. In the presence of ATP-Mg2+, a similar stepwise assembly is observed. However, at higher concentrations (30-75 µM), the average oligomeric size remains relatively unchanged around six subunits per oligomer. This is in sharp contrast with observations in ADP-Mg2+, where a marked decrease in the diffusion coefficient of Rca was observed, consistent with the formation of aggregates. The estimated K_d values obtained from the analysis of the FCS decays were similar for the first steps of the assembly process in both ADP-Mg2+ and ATP-Mg2+. However, the formation of the hexamer from the tetramer is much more favored in ATP-Mg2+, as evidenced from 20 fold lower K_d associated with this assembly step. This suggests that the formation of a hexameric ring in the presence of ATP-Mg2+. In addition to that, Rca aggregation is largely suppressed in the presence of ATP-Mg2+, as evidenced from the 1000 fold larger K_d value for the hexamer-24 mer association step. In essence, a fluorescence-based method was developed to monitor in vitro protein oligomerization and was successfully applied with Rca. The results provide a strong hint at the active oligomeric structure of Rca, and this information will hopefully help the ongoing research on the mechanistic enzymology of Rca.
ContributorsChakraborty, Manas (Author) / Levitus, Marcia (Thesis advisor) / Angell, Charles (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2014
Description
Biophysical techniques have been increasingly applied toward answering biological questions with more precision. Here, three different biological systems were studied with the goal of understanding their dynamic differences, either conformational dynamics within the system or oligomerization dynamics between monomers. With Cy3 on the 5' end of DNA, the effects of changing the terminal base pair were explored using temperature-dependent quantum yields. It was discovered, in combination with simulations, that a terminal thymine base has the weakest stacking interactions with the Cy3 dye compared to the other three bases. With ME1 heterodimers, the goal was to see if engineering a salt bridge at the dimerization interface could allow for control over dimerization in a pH-dependent manner. This was performed experimentally by measuring FRET between monomers containing either a Dap or an Asp mutation and comparing FRET efficiency at different pHs. It was demonstrated that the heterodimeric salt bridge would only form in a pH range near neutrality. Finally, with DNA processivity clamps, one aim was to compare the equilibrium dissociation constants, kinetic rate constants, and lifetimes of the closed rings for beta clamp and PCNA. This was done using a variety of biophysical techniques but with three as the main focus: fluorescence correlation spectroscopy, single-molecule experiments, and time-correlated single photon counting measurements. The stability of beta clamp was found to be three orders of magnitude higher when measuring solution stability but only one order of magnitude higher when measuring intrinsic stability, which is a result of salt bridge interactions in the interface of beta clamp. Ongoing work built upon the findings from this project by attempting to disrupt interface stability of different beta clamp mutants by adding salt or changing the pH of the solution. Lingering questions about the dynamics of different areas of the clamps has led to another project for which we have developed a control to demystify some unexpected similarities between beta clamp mutants. With that project, we show that single-labeled and double-labeled samples have similar autocorrelation decays in florescence correlation spectroscopy, allowing us to rule out the dyes themselves as causing fluctuations in the 10-100 microsecond timescale.
ContributorsBinder, Jennifer (Author) / Levitus, Marcia (Thesis advisor) / Wachter, Rebekka (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2015
Description
Geopolymers, a class of X-ray amorphous, ceramic-like aluminosilicate materials are produced at ambient temperatures through a process called geopolymerization. Due to both low energy requirement during synthesis and interesting mechanical and chemical properties, geopolymers are grabbing enormous attention. Although geopolymers have a broad range of applications including thermal/acoustic insulation and waste immobilization, they are always prepared in monolithic form. The primary aim of this study is to produce new nanostructured materials from the geopolymerization process, including porous monoliths and powders.
In view of the current interest in porous geopolymers for non-traditional applications, it is becoming increasingly important to develop synthetic techniques to introduce interconnected pores into the geopolymers. This study presents a simple synthetic route to produce hierarchically porous geopolymers via a reactive emulsion templating process utilizing triglyceride oil. In this new method, highly alkaline geopolymer resin is mixed with canola oil to form a homogeneous viscous emulsion which, when cured at 60 °C, gives a hard monolithic material. During the process, the oil in the alkaline emulsion undergoes a saponification reaction to decompose into water-soluble soap and glycerol molecules which are extracted to yield porous geopolymers. Nitrogen sorption studies indicates the presence of mesopores, whereas the SEM studies reveals that the mesoporous geopolymer matrix is dotted with spherical macropores. The method exhibits flexibility in that the pore structure of the final porous geopolymers products can be adjusted by varying the precursor composition.
In a second method, the geopolymerization process is modified to produce highly dispersible geopolymer particles, by activating metakaolin with sodium silicate solutions containing excess alkali, and curing for short duration under moist conditions. The produced geopolymer particles exhibit morphology similar to carbon blacks and structured silicas, while also being stable over a wide pH range.
Finally, highly crystalline hierarchical faujasite zeolites are prepared by yet another modification of the geopolymerization process. In this technique, the second method is combined with a saponification reaction of triglyceride oil. The resulting hierarchical zeolites exhibit superior CO2-sorption properties compared to equivalent commercially available and currently reported materials. Additionally, the simplicity of all three of these techniques means they are readily scalable.
In view of the current interest in porous geopolymers for non-traditional applications, it is becoming increasingly important to develop synthetic techniques to introduce interconnected pores into the geopolymers. This study presents a simple synthetic route to produce hierarchically porous geopolymers via a reactive emulsion templating process utilizing triglyceride oil. In this new method, highly alkaline geopolymer resin is mixed with canola oil to form a homogeneous viscous emulsion which, when cured at 60 °C, gives a hard monolithic material. During the process, the oil in the alkaline emulsion undergoes a saponification reaction to decompose into water-soluble soap and glycerol molecules which are extracted to yield porous geopolymers. Nitrogen sorption studies indicates the presence of mesopores, whereas the SEM studies reveals that the mesoporous geopolymer matrix is dotted with spherical macropores. The method exhibits flexibility in that the pore structure of the final porous geopolymers products can be adjusted by varying the precursor composition.
In a second method, the geopolymerization process is modified to produce highly dispersible geopolymer particles, by activating metakaolin with sodium silicate solutions containing excess alkali, and curing for short duration under moist conditions. The produced geopolymer particles exhibit morphology similar to carbon blacks and structured silicas, while also being stable over a wide pH range.
Finally, highly crystalline hierarchical faujasite zeolites are prepared by yet another modification of the geopolymerization process. In this technique, the second method is combined with a saponification reaction of triglyceride oil. The resulting hierarchical zeolites exhibit superior CO2-sorption properties compared to equivalent commercially available and currently reported materials. Additionally, the simplicity of all three of these techniques means they are readily scalable.
ContributorsMedpelli, Dinesh (Author) / Seo, Dong-Kyun (Thesis advisor) / Herckes, Pierre (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2015
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
Increasing concentrations of carbon dioxide in the atmosphere will inevitably lead to long-term changes in climate that can have serious consequences. Controlling anthropogenic emission of carbon dioxide into the atmosphere, however, represents a significant technological challenge. Various chemical approaches have been suggested, perhaps the most promising of these is based on electrochemical trapping of carbon dioxide using pyridine and derivatives. Optimization of this process requires a detailed understanding of the mechanisms of the reactions of reduced pyridines with carbon dioxide, which are not currently well known. This thesis describes a detailed mechanistic study of the nucleophilic and Bronsted basic properties of the radical anion of bipyridine as a model pyridine derivative, formed by one-electron reduction, with particular emphasis on the reactions with carbon dioxide. A time-resolved spectroscopic method was used to characterize the key intermediates and determine the kinetics of the reactions of the radical anion and its protonated radical form. Using a pulsed nanosecond laser, the bipyridine radical anion could be generated in-situ in less than 100 ns, which allows fast reactions to be monitored in real time. The bipyridine radical anion was found to be a very powerful one-electron donor, Bronsted base and nucleophile. It reacts by addition to the C=O bonds of ketones with a bimolecular rate constant around 1* 107 M-1 s-1. These are among the fastest nucleophilic additions that have been reported in literature. Temperature dependence studies demonstrate very low activation energies and large Arrhenius pre-exponential parameters, consistent with very high reactivity. The kinetics of E2 elimination, where the radical anion acts as a base, and SN2 substitution, where the radical anion acts as a nucleophile, are also characterized by large bimolecular rate constants in the range ca. 106 - 107 M-1 s-1. The pKa of the bipyridine radical anion was measured using a kinetic method and analysis of the data using a Marcus theory model for proton transfer. The bipyridine radical anion is found to have a pKa of 40±5 in DMSO. The reorganization energy for the proton transfer reaction was found to be 70±5 kJ/mol. The bipyridine radical anion was found to react very rapidly with carbon dioxide, with a bimolecular rate constant of 1* 108 M-1 s-1 and a small activation energy, whereas the protonated radical reacted with carbon dioxide with a rate constant that was too small to measure. The kinetic and thermodynamic data obtained in this work can be used to understand the mechanisms of the reactions of pyridines with carbon dioxide under reducing conditions.
ContributorsRanjan, Rajeev (Author) / Gould, Ian R (Thesis advisor) / Buttry, Daniel A (Thesis advisor) / Yarger, Jeff (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2015
Description
Transparent conductive oxides (TCO) comprise a class of materials that exhibit unique combination of high transparency in the visible region along with high electrical conductivity. TCOs play an important role as transparent electrodes for optoelectronic devices such as solar cell panels, liquid crystal displays, transparent heat mirrors and organic light emitting devices (OLED). The most commonly used transparent electrodes in optoelectronic applications is indium tin oxide (ITO) due to its low resistivity (~ 10−4 Ω-cm) and high transmittance (~ 80 %). However, the limited supply of indium and the growing demand for ITO make the resulting fabrication costs prohibitive for future industry. Thus, cost factors have promoted the search for inexpensive materials with good electric-optical properties.
The object of this work is to study the structure-property-processing relationship and optimize a suitable transparent electrode with the intent to optimize them for flexible optoelectronics applications. The work focuses on improved processing of the mixed oxide (indium gallium zinc oxide, IGZO) thin films for superior optical and electrical properties. The study focuses on two different methods of post-deposition annealing-microwave and conventional. The microwave annealing was seen to have the dual advantage of reduced time and lower temperature, as compared to conventional annealing. Another work focuses on an indium free transparent composite electrode (TCE) where a very thin metal layer is inserted between the two TCO layers. A novel Nb2O5/Ag/Nb2O5 multilayered structure can exhibit better electrical and optical properties than a single layered TCO thin film. The focus for low cost alternative leads to a TiO2/metal/TiO2 based TCE. A systematic study was done to understand the effect of metal thickness and substituting different metals (Ag, Cu or Au) on the opto-electrical properties of the TCEs. The TiO2/Ag/TiO2 with mid Ag thickness 9.5 nm has been optimized to have a sheet resistance of 5.7 Ohm/sq. average optical transmittance of 90 % at 550 nm and figure of merit with 61.4 ×10-3 Ω-1. The TCEs showed improved optical and electrical properties when annealed in forming gas and vacuum. These dielectric/metal/dielectric multilayer TCEs have lower total thickness and are more efficient than a single-layer ITO film.
The object of this work is to study the structure-property-processing relationship and optimize a suitable transparent electrode with the intent to optimize them for flexible optoelectronics applications. The work focuses on improved processing of the mixed oxide (indium gallium zinc oxide, IGZO) thin films for superior optical and electrical properties. The study focuses on two different methods of post-deposition annealing-microwave and conventional. The microwave annealing was seen to have the dual advantage of reduced time and lower temperature, as compared to conventional annealing. Another work focuses on an indium free transparent composite electrode (TCE) where a very thin metal layer is inserted between the two TCO layers. A novel Nb2O5/Ag/Nb2O5 multilayered structure can exhibit better electrical and optical properties than a single layered TCO thin film. The focus for low cost alternative leads to a TiO2/metal/TiO2 based TCE. A systematic study was done to understand the effect of metal thickness and substituting different metals (Ag, Cu or Au) on the opto-electrical properties of the TCEs. The TiO2/Ag/TiO2 with mid Ag thickness 9.5 nm has been optimized to have a sheet resistance of 5.7 Ohm/sq. average optical transmittance of 90 % at 550 nm and figure of merit with 61.4 ×10-3 Ω-1. The TCEs showed improved optical and electrical properties when annealed in forming gas and vacuum. These dielectric/metal/dielectric multilayer TCEs have lower total thickness and are more efficient than a single-layer ITO film.
ContributorsDhar, Aritra (Author) / Alford, Terry L. (Thesis advisor) / Petuskey, William (Thesis advisor) / Krause, Stephen (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2015
Description
Chloroform (CHCl3) is an important atmospheric pollutant by its direct health effects as well as by its contribution to photochemical smog formation. Chloroform outgassing from swimming pools is not typically considered a source of atmospheric CHCl3 because swimming pools are scarce compared to other sources. However, large urban areas in hot climates such as Phoenix, AZ contain a substantial amount of swimming pools, potentially resulting in significant atmospheric fluxes. In this study, CHCl3 formation potential (FP) from disinfection of swimming pools in Phoenix was investigated through laboratory experiments and annual CHCl3 emission fluxes from swimming pools were estimated based on the experimental data.
Swimming pool water (collected in June 2014 in Phoenix) and model contaminants (Pharmaceuticals and Personal Care Products (PPCPs), Endocrine Disrupting Compounds (EDCs), artificial sweeteners, and artificial human waste products) were chlorinated in controlled laboratory experiments. The CHCl3 production during chlorination was determined using Gas Chromatography-Mass Spectrometry (GC-MS) following solid-phase microextraction (SPME). Upon chlorination, all swimming pool water samples and contaminants produced measureable amounts of chloroform. Chlorination of swimming pool water produced 0.005-0.134 mol CHCl3/mol C and 0.004-0.062 mol CHCl3/mol Cl2 consumed. Chlorination of model contaminants produced 0.004-0.323 mol CHCl3/mol C and 0.001-0.247 mol CHCl3/mol Cl2 consumed. These numbers are comparable and indicate that the model contaminants react similarly to swimming pool water during chlorination. The CHCl3 flux from swimming pools in Phoenix was estimated at approximately 3.9-4.3 Gg/yr and was found to be largely dependent on water temperature and wind speed while air temperature had little effect. This preliminary estimate is orders of magnitude larger than previous estimates of anthropogenic emissions in Phoenix suggesting that swimming pools might be a significant source of atmospheric CHCl3 locally.
Swimming pool water (collected in June 2014 in Phoenix) and model contaminants (Pharmaceuticals and Personal Care Products (PPCPs), Endocrine Disrupting Compounds (EDCs), artificial sweeteners, and artificial human waste products) were chlorinated in controlled laboratory experiments. The CHCl3 production during chlorination was determined using Gas Chromatography-Mass Spectrometry (GC-MS) following solid-phase microextraction (SPME). Upon chlorination, all swimming pool water samples and contaminants produced measureable amounts of chloroform. Chlorination of swimming pool water produced 0.005-0.134 mol CHCl3/mol C and 0.004-0.062 mol CHCl3/mol Cl2 consumed. Chlorination of model contaminants produced 0.004-0.323 mol CHCl3/mol C and 0.001-0.247 mol CHCl3/mol Cl2 consumed. These numbers are comparable and indicate that the model contaminants react similarly to swimming pool water during chlorination. The CHCl3 flux from swimming pools in Phoenix was estimated at approximately 3.9-4.3 Gg/yr and was found to be largely dependent on water temperature and wind speed while air temperature had little effect. This preliminary estimate is orders of magnitude larger than previous estimates of anthropogenic emissions in Phoenix suggesting that swimming pools might be a significant source of atmospheric CHCl3 locally.
ContributorsRose, Christy J (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew (Committee member) / Hayes, Mark (Committee member) / Westerhoff, Paul (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
Nucleosomes are the basic repetitive unit of eukaryotic chromatin and are responsible for packing DNA inside the nucleus of the cell. They consist of a complex of eight histone proteins (two copies of four proteins H2A, H2B, H3 and H4) around which 147 base pairs of DNA are wrapped in ~1.67 superhelical turns. Although the nucleosomes are stable protein-DNA complexes, they undergo spontaneous conformational changes that occur in an asynchronous fashion. This conformational dynamics, defined by the "site-exposure" model, involves the DNA unwrapping from the protein core and exposing itself transiently before wrapping back. Physiologically, this allows regulatory proteins to bind to their target DNA sites during cellular processes like replication, DNA repair and transcription. Traditional biochemical assays have stablished the equilibrium constants for the accessibility to various sites along the length of the nucleosomal DNA, from its end to the middle of the dyad axis. Using fluorescence correlation spectroscopy (FCS), we have established the position dependent rewrapping rates for nucleosomes. We have also used Monte Carlo simulation methods to analyze the applicability of FRET fluctuation spectroscopy towards conformational dynamics, specifically motivated by nucleosome dynamics. Another important conformational change that is involved in cellular processes is the disassembly of nucleosome into its constituent particles. The exact pathway adopted by nucleosomes is still not clear. We used dual color fluorescence correlation spectroscopy to study the intermediates during nucleosome disassembly induced by changing ionic strength. Studying the nature of nucleosome conformational change and the kinetics is very important in understanding gene expression. The results from this thesis give a quantitative description to the basic unit of the chromatin.
ContributorsGurunathan, Kaushik (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Woodbury, Neal (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011