Dan Bizzotto

DNA electrochemical (E-DNA) biosensor has developed rapidly and gained worldwide attention from many fields such as medical science, food industry, and environmental analysis. However, current electrochemical DNA biosensors have a few critical limitations that prevent E-DNA sensors from becoming more valuable and useful for commercial applications. This thesis addresses some of the issues of E-DNA biosensors such as thermal stability and functionality using electrochemistry and in-situ fluorescence microscopy. The work in this thesis used single crystal gold bead electrode as the substrate which provided a great opportunity to build the near ideal DNA SAMs with far less defects than on the polycrystalline gold which is typically used in the sensor fabrication. Together with the single crystal Au bead as the substrate and in-situ fluorescence microscopy, a thorough investigation on the properties of DNA SAMs prepare with and without potential control (Edep vs. OCPdep) was conducted. The results demonstrated Edep with superior thermal stability in solution and higher sensitivity than OCPdep. A detailed analysis on the influence of surface crystallography on the thermal stability and the packing behavior of both types of DNA SAMs prepared by Edep and OCPdep was also provided.

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Deoxyribonucleic acid (DNA) self-assembled monolayers (SAMs) immobilized on gold electrodes are the basis of many electrochemical biosensors. Control of the interfacial behavior of DNA by means of an electric field is of interest for sensing applications such as the detection of single nucleotide polymorphisms (SNPs). Moreover, the in situ characterization of immobilized DNA monolayers at a molecular level is important for the fabrication of robust, reliable and sensitive sensors.The thesis aims at studying the discrimination between DNA strands containing SNPs on the basis of electric-field assisted hybridization/denaturation of DNA. In situ electrochemical fluorescence microscopy is used as a detection methodology and characterization tool for DNA interfaces. For this purpose, fluorescently labeled DNA sequences are immobilized at gold electrodes as thiol SAMs.First, the SAMs under investigation were composed of perfect match or SNP-containing target sequences. The relationship between the applied potential and the denaturation of DNA duplexes was investigated. Electrochemical melting was observed at -0.25 V vs. Ag|AgCl and attributed to an electrostatics-based melting mechanism. A model based on electrical double layer theories was proposed to explain the observed partial electrochemical melting. The influence of various parameters was systematically investigated such as the assembly of the SAM and the measurement conditions. The observed trends were attributed to a destabilization of the duplex. The most influential variables were the DNA sequence (e.g. mismatch near the electrode surface), ionic strength and temperature. Next, a FRET methodology was investigated by studying a model DNA SAM system labeled with a FRET pair. The aim of the study was to gain information regarding the local molecular scale environment of a DNA SAM under measurement conditions. The influence of surface crystallography on the SAM organization was studied by wide-field FRET microscopy. FRET measurements were used in a semi quantitative way to characterize the uniformity of the DNA monolayer. A departure from the ideal uniform DNA distribution was observed for the (111) and (110) surface regions. The study provided a proof of concept for the use of electrochemical FRET microscopy as an in situ characterization tool for DNA modified electrode surfaces.

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Deoxyribonucleic acid (DNA) self-assembled monolayers (SAMs) consist of bioelectronic interfaces that have been proposed for use as DNA biosensors. These are portable medical device used for diagnosing diseases through specific detection of biomolecules. These DNA SAMs are composed of chemically modified DNA molecules adsorbed onto gold surfaces and are made by immersing a gold surface in a solution of thiol-modified DNA. Previous literature has shown that an applied potential to the gold surface during the DNA immersion enhances DNA SAM formation by decreasing self-assembly time and forming DNA SAMs of higher quality. These electrodeposited DNA SAMs were observed using average measurement techniques on the entire surface. These averaged techniques are unable to characterize heterogeneous features in DNA SAMs. Instead, an imaging technique such as in-situ electrochemical fluorescence microscopy (iSEFMI) can be used to investigate these electrodeposited DNA SAMs.In this work, DNA SAMs were electrodeposited onto single crystal bead electrodes. These electrodes were key for examining DNA SAMs on different surface crystallographies (ie. surface atomic arrangements). Using iSEFMI, the electrodeposited DNA SAMs on the single crystal bead electrodes were characterized, with DNA coverage measurements on each surface crystallography possible. It was established that applying either negative or positive potentials resulted in DNA SAMs of high coverage with positive potentials resulting in more uniform DNA coverages across all surface crystallographies. Applying a modulating potential further created DNA SAMs of slightly higher DNA coverages. The effect of an applied potential on DNA SAMs adsorbing onto different surface crystallographies was also investigated. Both a constant potential and a modulating square wave potential will be applied and the resulting DNA SAMs studied. The presence of specifically adsorbing anions in solution was found to affect both the gold surface and the potential-assisted DNA deposition resulting in a DNA SAM of unusual character. Understanding the factors that affect potential-assisted DNA deposition will enable the formation of an optimal procedure for manufacturing DNA SAMs. With the appropriate variables controlled, DNA SAMs can be tailored for their application in DNA biosensors and eventual use in point-of-care devices.

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The complex interface between polymer electrolytes and nanostructured electrodes is key for the operation of many electrochemical devices. While the surface science of electrocatalysts have been extensively studied using simplified model systems, such as Pt single crystals, the extent to which lessons from these models apply to nanostructured interfaces remains poorly understood. In this work, the interface between Pt nanoparticles and solid polymer electrolytes is explored in terms of catalytic activity, morphology and durability. The nucleation and growth of nanoparticles is controlled to produce contiguous ultrathin catalyst layers in a solution processable fashion using electroless deposition. The reactivity and structure of the Pt-polymer surface was probed with advanced characterization techniques using synchrotron radiation. Direct imaging of the solid-electrolyte-interphase was accomplished with X-ray spectromicroscopy. Degradation of this interface was visible after a simulated aging protocol. Finally, the mechanism of surface oxidation and reduction on Pt nanoparticles was explored with diffraction, moving towards an atomistic understanding of fuel cell electrochemistry inside functional devices under relevant operational conditions.

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Self-assembled monolayers (SAMs) are important structures commonly employed to functionalize metal surfaces. To optimize a metal-SAM construct, it is important to characterize the influence of the surface crystallography. In this thesis, a single crystal Au bead electrode was employed to investigate different types of SAMs, enabling studies on a variety of surfaces under identical conditions and avoiding laborious experimental replicates on a large number of crystal orientations.The application of a single crystal Au bead electrode was demonstrated by investigating the reductive desorption process for two types of SAM: the alkanethiolate SAM and the α-aminoisobutyric acid (Aib) peptide thiolate SAM. Using in situ fluorescence imaging, the influence of surface crystallography on reductive desorption was observed, reflected as a correlation between the density of broken bonds of a surface and the reductive desorption potential of a SAM deposited on the surface. Besides the surface crystallography, intermolecular interactions also had a significant impact on determining the desorption potential.Aib peptide thiolate SAMs on a Au(111) facet were further investigated. It was found that the low packing density Aib peptide thiolate SAMs exhibited a potential-modulated fluorescence response which was believed to be due to the orientational or structural change of the peptide molecules in response to the applied potential.The potential-driven reorientation effect of the DNA SAMs has been intensively explored due to its application in biosensing. Characterization of the DNA SAMs with in situ fluorescence methods suggested that surface crystallography exerts an influence not only on the formation of the DNA SAMs but also on the efficiency of the potential-driven response. Moreover, a spectroelectrochemical technique that couples electrochemistry, fluorescence microscopy and harmonic analysis was developed to explore the non-linearity of the fluorescence response to an applied AC potential. This technique could be potentially applied to detect changes in DNA hybridization state.The experimental results demonstrate the convenience and wide applicability of using a single crystal Au bead electrode to investigate SAMs. On the other hand, applying existing and developing new spectroelectrochemical techniques give insights into creating SAMs with desirable properties.

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Thin organic layers deposited on electrodes are ubiquitously proposed for a variety of surface-related applications. The quality of these layers is usually assessed by analytical methods that average the measured signal over a large area compared to the molecular scale. This work outlines the use of in-situ fluorescence microscopy as a characterization method by analyzing three examples of such layers.First, a heterogeneous Langmuir layer was physically adsorbed to a gold electrode via the Langmuir-Schaefer method and the effects of the substrate analyzed by comparing the adsorbed layer with the predecessor floating film. Through the use of a dimer-forming fluorophore, substrate mediated condensation was suggested.Second, the reductive desorption of self-assembled monolayers (SAMs) from microelectrodes was used to investigate the movement of the released thiolate molecules. Once in solution, these molecules were found to follow a buoyant movement, consequence of the high local concentration of H₂ resulting from the simultaneous reduction of water under the conditions employed.Finally, a DNA SAM system that has been previously suggested as a biosensing platform was investigated for heterogeneity. It was found that the substrate crystallography had a significant effect on the density and efficiency of potential driven change in conformation of the immobilized probes. Furthermore, a deconvolution method is proposed in order to correct for the effect of the electrode charging time constant on the measurements of the kinetics of the DNA conformation change.Overall, the performed experiments show that in-situ fluorescence microscopy is a useful technique to analyze distance dependent phenomena involving these deposited layers. Moreover, the coupling between electrochemistry and fluorescence allows not only to monitor but also to drive changes in the layers, creating systems capable of studying the dynamics of the deposited films.The inclusion of the proposed technique as a characterization tool during the development of systems based on ultrathin organic films could improve the understanding of the influence of the deposition conditions on the film quality, helping to attain the necessary robustness to make the proposed systems actually achieve their proposed applications.

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Transmembrane proteins and ion channels are a major target for new drug development.Incorporating them into sensors requires a method to produce stable, easilymodifiable solid-supported phospholipid bilayers. This thesis demonstrates amethod for using potential control on the electrode to mediate liposome adsorption,allowing them to interact with a previously deposited octadecanol layer throughpotential-created defects.Compression isotherms and electrochemical measurements were used to establishthe effect of the incorporation of a small amount of fluorescent dye on theoctadecanol layers. Using these fluorescently-labelled octadecanol layers, electrochemicalmeasurements both independently and coupled with in-situ fluorescencemeasurements were used to characterize the interaction of liposomes with theselayers under potential control. It was found that application of moderate potentials- more negative than the onset of defect formation but less than that required fordesorption of the layer - facilitated the effective incorporation of liposome materialinto the octadecanol bilayer. The length of time spent at the poration potential hadlittle effect on the degree of liposome interaction with the adsorbed layer. The incorporationwas seen as a change in the double-layer capacitance and the creationof small fluorescent structures in the layer after exposure to liposomes at the porationpotential. A shift in the characteristic desorption potential was also seen withliposome incorporation.Atomic force microscopy coupled in-situ with electrochemical control was alsoused to investigate the interaction of liposomes with the adsorbed octadecanol layer.The structure of the adsorbed layer was observed and with liposomes present insolution, the creation of three-dimensional structures similar in nature to those seenby fluorescence was noted. The incorporation of liposomes into the octadecanolwas shown to be easily controlled by application of an electrical potential, openinga path for a new method of producing supported lipid bilayers in-situ for biosensingapplications.

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Copper interconnects in advanced integrated circuits are manufactured by processes that include electrodeposition, chemical mechanical polishing and annealing. The as-deposited copper is nano-crystalline and undergoes a microstructure evolution at room temperature (self-annealing) or during an annealing step. During this process, significant changes in resistivity and grain size are observed. In this work, the microstructure evolution in 0.5-3 μm-thick electrodeposited copper thin films was studied. Resistivity measurements were used to quantify the role of deposition conditions on the microstructure evolution rate. In-situ electron backscatter diffraction (EBSD) was employed to observe self-annealing at the film surface. The resistivity-microstructure correlation during self-annealing was examined. A phenomenological model using the Johnson-Mehl-Avrami-Kolmogorov (JMAK) approach was developed to describe recrystallization during isothermal and continuous annealing treatments. The microstructure evolution in copper-silver alloys and films produced by variable deposition rates was investigated. Phase-field model was applied to simulate self-annealing and the effect of deposition current density.The results show that the drop in resistivity during self-annealing is accompanied by significant changes of the microstructure at the film surface. Different criteria were developed to assess self-annealing rate from EBSD maps including grain size, image quality and local orientation spread. Adopting a grain size threshold, it was found that there is a reasonable correlation between resistivity and microstructure during self-annealing. The recrystallization in copper thin films appears to be thermally activated with an activation energy of 0.89-0.93 eV. Adopting the principle of additivity, it was found that the recrystallization rate during continuous annealing can be described by the JMAK model using the isothermal resistivity profiles. A method was proposed to accelerate recrystallization based on a capping layer deposition. No recrystallization was observed when silver was co-deposited with copper in the absence of chloride (even when annealed at 100 °C for 5 hours). Phase-field model was able to describe self-annealing and the effect of deposition current density. The results in this thesis are of significance to the microelectronic industry where recrystallization is a crucial step in the fabrication of copper interconnects for the high performance integrated circuits.

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No abstract available.

No abstract available.