In recent years, semiconductor quantum dots (QDs) have arisen as a new class of fluorescent probes that possess unique optical and electronic properties well-suited for single-molecule imaging of dynamic live cell processes. Nonetheless, the large size of conventional QD-ligand constructs has precluded their widespread use in single-molecule studies, especially on cell interiors. A typical QD-ligand construct can range upwards of 35 nm in diameter, well exceeding the size threshold for cytosolic diffusion and posing steric hindrance to binding cell receptors. The objective of this research is to develop tagging strategies that allow QD-ligand conjugates to specifically bind their target proteins while maintaining a small overall construct size. To achieve this objective, we utilize the HaloTag protein (HTP) available from Promega Corporation, which reacts readily with a HaloTag ligand (HTL) to form a covalent bond. When HaloTag ligands are conjugated to size-minimized multidentate polymer coated QDs, compact QD-ligand constructs less than 15 nm in diameter can be produced. These quantum dot-HaloTag ligand (QD-HTL) conjugates can then be used to covalently bind and track cellular receptors genetically fused to the HaloTag protein. In this study, size-minimized quantum dot-HaloTag ligand conjugates are synthesized and evaluated for their ability to bind specifically to purified and cellular HTP. The effect of QD-HTL surface modifications on different types of specific and nonspecific cellular binding are systematically investigated. Finally, these QD-HTL conjugates are utilized for single-molecule imaging of dynamic live cell processes. Our results show that size-minimized QD-HTLs exhibit great promise as novel imaging probes for live cell imaging, allowing researchers to visualize cellular protein dynamics in remarkable detail.

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RNA nanotechnology is an emerging field that holds great promise for advancing drug delivery and materials science. Recently, RNA nanoparticles have seen increased use as an in vivo delivery system. RNA was once thought to have little potential for in vivo use due to biological and thermodynamic stability issues. However, these issues have been solved by: (1) Finding of a thermodynamically stable three-way junction (3WJ) motif; (2) Chemical modifications to RNA confer enzymatic stability in vivo; and (3) the finding that RNA nanoparticles exhibit low immunogenicity in vivo. In vivo biodistribution and pharmacokinetics are affected by the physicochemical properties, such as size, shape, stability, and surface chemistry/properties, of the nanoparticles being delivered. RNA has an inherent advantage for nanoparticle construction as each of these properties can be finely tuned. The focus of this study is as follows: (1) Construction of diverse size and shape RNA nanoparticles with tunable physicochemical properties; (2) Investigation of the effect that size, shape, and nanoparticle properties have on in vivo biodistribution; (3) Development of drug encapsulation and release mechanism utilizing RNA nanotechnology; and (4) Establishment of large-scale synthesis and purification methods of RNA nanoparticles. In (1), RNA triangle, square, and pentagon shaped nanoparticles were constructed using the phi29 pRNA-3WJ as a core motif. Square nanoparticles were constructed with sizes of 5, 10, and 20 nanometers. The RNA polygons were characterized by AFM to demonstrate formation of their predicted geometry per molecular models. Furthermore, the properties of RNA polygons were tuned both thermodynamically and chemically by substitution of nucleic acid type used during nanoparticle assembly. In (2), the biodistribution of RNA nanosquares of diverse sizes and RNA polygons of diverse shapes were investigated using tumor models in nude mice. It was found that increasing the size of the nanosquares led to prolonged circulation time in vivo and higher apparent accumulation in the tumor. However, it was observed that changing of shape had little effect on biodistribution. Furthermore, the effect of the hydrophobicity on RNA nanoparticles biodistribution was examined in mouse models. It was found that incorporation of hydrophobic ligands into RNA nanoparticles causes non-specific accumulation in healthy organs, while incorporation of hydrophilic ligands does not. Lower accumulation in vital organs of hydrophobic chemicals was observed after conjugation to RNA nanoparticles, suggesting RNA has the property to solubilize hydrophobic chemicals and reduce accumulation and toxicity in vital organs. In (3), a 3D RNA nanoprism was constructed to encapsulate a small molecule fluorophore acting as a model drug. The fluorophore was held inside the nanoprism by binding to an RNA aptamer. The ability of the stable frame of the nanoprism to protect the fragile aptamer inside was evidenced by a doubling of the fluorescent half-life in a degrading environment. In (4), a method for large-scale in vitro synthesis and purification of RNA nanoparticles was devised using rolling circle transcription (RCT). A novel method for preparing circular double stranded DNA was developed, overcoming current challenges in the RCT procedure. RCT produced more than 5 times more RNA nanoparticles than traditional run-off transcription, as monitored by gel electrophoresis and fluorescence monitoring. Finally, large-scale purification methods using rate-zonal and equilibrium density gradient ultracentrifugation, as well as gel electrophoresis column, were developed.

We developed new methods for controlling and studying microtubules (MTs) outside the complex workings of the living cell. Several surface treatments for preventing MT fouling on surfaces were analyzed and, for the first time, a self-assembled monolayer (SAM) was developed which prevented MT adsorption in the absence of passivating proteins. The morphology and thickness of the SAM was measured to determine the mechanism of formation and origin of the MT-resistant behavior. The SAM was integrated into electron beam lithography for patterning and manipulating MTs using electrophoresis. Reversible MT adsorption and patterning and alignment of single MTs were achieved. We characterized the mechanism for the MT migration under electric field with a focus on the electrodynamics of the flow cell and the forces acting on the MT, along with the time dependence of the process.

Nanofabrication techniques were used to manufacture nanometer scale protein templates. The fabrication approach employs electron beam lithography (EBL) patterning on poly(ethylene glycol) (PEG) thiol (CH3O(CH2CH2O)17NHCO(CH2)2SH) self-assembled monolayers (SAM) on Au. The PEG SAM prevented protein surface adhesion and binding sites for protein were created in the SAM by EBL. Subsequent to EBL, the patterns in the PEG SAM were backfilled with 40-nm NeutrAvidin-coated fluorescent spheres (FluoSpheres). The spontaneous and directed immobilization of the spheres from a solution to the patterns resulted in high resolution protein patterns. The FluoSpheres could be arranged in any arbitrary pattern with ultimately only one or a few FluoSpheres at each binding site. Growth dynamics and SAM morphology of PEG on Au were studied by atomic force microscopy (AFM). PEG SAMs on three types of Au with different microstructure were examined: thermally evaporated granular Au and two types of Au films produced by hydrogen flame annealing of granular Au, Au(111) and "terraced" Au (crystal orientation unknown). The different Au surfaces' substructure affected the morphology and mechanical properties of the PEG SAM. On Au(111), AFM imaging revealed monolayer formation through three distinct steps: island nucleation, island growth, and coalescence. The fine-structure of the SAM revealed dendritic island formation - an observation which can be explained by attractive intermolecular interactions and diffusion-limited aggregation. Island growth was not observed on the "terraced" Au. AFM studies of EBL patterned PEG SAMs on Au(111) revealed two different patterning mechanisms. At low doses, the pattern formation occurs by SAM ablation in a self-developing process where the feature depth is directly dose dependent. At higher doses electron beam induced deposition of material, so-called contamination writing, is seen in the ablated areas of the SAM. The balance between these two mechanisms is shown to depend on the geometry of the pattern. In addition to PEG SAMs, fibronectin monolayers on SiO2 surfaces were patterned by EBL. The areas exposed with EBL lose their functionality and do not bind anti-fibronectin. With this approach we constructed fibronectin templates and used them for cell studies demonstrating pattern dependent cell geometries and cell adhesion. / QC 20101008

<p>Nanofabrication techniques were used to manufacture nanometer scale protein templates. The fabrication approach employs electron beam lithography (EBL) patterning on poly(ethylene glycol) (PEG) thiol (CH3O(CH2CH2O)17NHCO(CH2)2SH) self-assembled monolayers (SAM) on Au. The PEG SAM prevented protein surface adhesion and binding sites for protein were created in the SAM by EBL. Subsequent to EBL, the patterns in the PEG SAM were backfilled with 40-nm NeutrAvidin-coated fluorescent spheres (FluoSpheres). The spontaneous and directed immobilization of the spheres from a solution to the patterns resulted in high resolution protein patterns. The FluoSpheres could be arranged in any arbitrary pattern with ultimately only one or a few FluoSpheres at each binding site.</p><p>Growth dynamics and SAM morphology of PEG on Au were studied by atomic force microscopy (AFM). PEG SAMs on three types of Au with different microstructure were examined: thermally evaporated granular Au and two types of Au films produced by hydrogen flame annealing of granular Au, Au(111) and "terraced" Au (crystal orientation unknown). The different Au surfaces' substructure affected the morphology and mechanical properties of the PEG SAM. On Au(111), AFM imaging revealed monolayer formation through three distinct steps: island nucleation, island growth, and coalescence. The fine-structure of the SAM revealed dendritic island formation - an observation which can be explained by attractive intermolecular interactions and diffusion-limited aggregation. Island growth was not observed on the "terraced" Au.</p><p>AFM studies of EBL patterned PEG SAMs on Au(111) revealed two different patterning mechanisms. At low doses, the pattern formation occurs by SAM ablation in a self-developing process where the feature depth is directly dose dependent. At higher doses electron beam induced deposition of material, so-called contamination writing, is seen in the ablated areas of the SAM. The balance between these two mechanisms is shown to depend on the geometry of the pattern.</p><p>In addition to PEG SAMs, fibronectin monolayers on SiO2 surfaces were patterned by EBL. The areas exposed with EBL lose their functionality and do not bind anti-fibronectin. With this approach we constructed fibronectin templates and used them for cell studies demonstrating pattern dependent cell geometries and cell adhesion.</p>

<p>Nanotechnology has experienced a tremendous rise in the last decade. The synthesis of nanomaterials of defined structure and controlled properties is one of the most challenging part. Solution processing bottom-up fabrication techniques enables the facile synthesis of low dimension and ordered structures with low cost through the self-assembly of basic building blocks. Biotemplating has become an emerging field in which natural biomolecular objects are utilized for creating functional, hierarchical, controlled patterned structures with nanometric precision. It is a capital effective, eco-friendly and energy-efficient synthetic process. Viral biotemplating has shown great potential in electronics, environmental and biomedical devices. In recent years, in-planta produced Tobacco Mosaic Virus (TMV) and its variants have been used to produce metal nanorods and nanowires of monodisperse structures under mild conditions without the use of harsh chemical treatments although there remains much to be understood. Mass production of biotemplate, programming of viral particles of desired functionalities, manipulation for biomineralized metal materials of good quality have not been sufficiently studied to allow for directed synthesis. The fundamental studies on platform development for viral biotemplate production, design of viral proteins carrying engineered properties, and the hydrothermal synthesis of biotemplated metal nanomaterials, which create great uniformity and high coverage are of interest in this dissertation. Three experimental studies are outlined.<br></p><p><br></p><p>A novel virus biotemplate, Barley stripe mosaic virus (BSMV) virus-like particle is designed and engineered through genetic engineering. By fusing the Origin of Assembly from TMV to the transcript encoding BSMV capsid protein, the self-assembly of BSMV-VLP nanorod from microbial-based protein expression system was achieved for the first time. An alternate platform for viral particle production has been developed. Optimization of VLP expression, purification and processing conditions are performed. This developed alternative E. coli production platforms offer unique opportunities for genetic engineering and faster protein expression; therefore, the development of our system enables rapid design-build-test cycles for the engineering and production of BSMV-VLPs with desired properties. Results in this project shows the power of genetic engineering and serves as a springboard for genetic engineering of the VLPs.<br></p><p><br></p><p>Programming on BSMV-VLP is further used to decouple the VLP assembly into governing internal molecular interactions. To drive the nucleic acid free helical BSMV-VLP rod assembly and further increase the stability of capsid proteins, an identification of Caspar Carboxylate cluster in BSMV is performed. Various carboxylate residues were selected through protein crystal structure and examined systematically through experimental work. By introducing mutations on selected residues, the intersubunit carboxylate interaction of the proteins was significantly altered, resulting in an in vivo production of nucleic-acid free BSMV-VLP assembly for the first time. The change in interactions leads to increased stability of the modified VLP, enabling the formation of longer nanorods with lengths over one micrometer. Moreover, both wild-type and mutated BSMV-VLPs were shown to have great structural stability across a wide range of pHs. Overall, we exhibit experimental identification to systematically probe the key carboxylate interactions to increase the stability of proteins and drive RNA-free BSMV-VLP assembly. This project greatly expands the potential usefulness of the engineered BSMV-VLP biotemplates for a wide variety of applications.<br></p><p><br></p><p>Finally, to demonstrate the versatile uses of BSMV-VLP in biotemplating, the new biotemplate was utilized to expand understandings on the directed synthesis of metal nanostructures. By using the hydrothermal synthesis, VLPs were successfully utilized to synthesize monometallic palladium nanorods with a wide range of length scales. The VLP-mediated nanorods are more uniformly and fully-covered than the ones synthesized with in planta-produced BSMV virion. Besides, the synthesis shows an effective control over the metal nanorod diameter. The capability of BSMV-VLP was readily expanded from the synthesis of monometallic nanorods to bimetallic hybrid. In the absence of an exogenous reducing agent, mineralization of platinum, gold and copper was successfully demonstrated on the VLP. It is attributed to lower reduction barrier introduced by already-deposited palladium nanoparticles which serve as nucleation sites for subsequent metal reduction. The formation of bimetallic complexes was further supported by STEM, EDS and XPS analysis evidenced the presences of multiple metals. Overall, BSMV-VLP-mediated biotemplating using the hydrothermal synthesis has been confirmed to be a promising and feasible approach to create organic-inorganic complex nanocomposite.<br></p><p><br></p><p>Lastly, to move toward an application, the synthesized Pd nanorods coated with full coverage and great uniformity of nanoparticles were utilized as an exciting hydrogen sensing material. The developed hydrogen sensing system using a quartz crystal microbalance shows a fast response toward hydrogen as well as the ability of hydrogen detection and quantification of the adsorption capacity. This study serves as an entry point and opens up enormous possibility for next-generation of Pd-virus hybrid hydrogen sensors.<br></p><p><br></p><p>Taken together, this dissertation has demonstrated the engineering and production of a novel BSMV virus-like particle bacterial system. This alternative platform and developed parameter space for VLP production is genetically tractable and requires significantly shorter processing duration for large-scale and mass production. The BSMV-VLP biotemplated metal nanomaterials present great qualities and controllable dimensions. This approach has explored the synthetic palette and opened up enormous possibilities in the bottom-up nanofabrication of versatile and tunable organic-inorganic nanoscaled complex and would facilitate future engineering industrial applications.<br></p>

Over the past few decades, inorganic nanostructured materials have elicited a lot of interest due to their high surface-to-volume ratio and many size dependent properties which stem from their nanoscale dimensions. Owing to these distinct properties, they have found applications in widespread fields like catalysis, energy storage, electronics, and biotechnology. In the field of biotechnology, nanotubes and mesoporous materials are attractive vehicles for drug delivery because of their hollow and porous structures and facile surface functionalization. Their inner void can take up large amounts of drug as well as act as gates for the controlled release of drug. These hollow structures can also be used for confining biomolecules like proteins and peptides. The study on protein conformation in biocompatible materials is very important in materials sciences for the development of new and efficient biomaterials(sensors, drug delivery systems or planted devices). Titania(TiO2)has been widely explored for applications in photovoltaic cells, batteries, desalination, sensing, and photocatalysis, to name only a few. The work presented in this thesis focuses on titania based nanostructures for drug delivery and protein confinement. First part of the work focusses on synthesis and characterization of Fe-doped TiO2 nanotubes. Fe-doped TiO2 nanotubes were demonstrated as controlled drug delivery agents. In vitro cytotoxic effects of Fe-doped titania nanotubes were assessed by MTT assay by exposing Hela cell line to the nanotubes. Second part of the work focusses on synthesis and characterization of TiO2 nanotubes by two synthesis procedures, namely hydrothermal and sol-gel template synthesis. Myoglobin, a model globin protein was encapsulated in hydrothermally synthesized TiO 2 nanotubes(diameter 5 nm) and sol-gel template synthesized TiO2 nanotubes(diameter 200 nm). Effect of encapsulating myoglobin these nanotubes was studied. The electrochemical activity and structure of myoglobin were studied by cyclic voltammetry and circular dichroism respectively. Direct electron transfer was found to be enhanced upon confinement in 200 nm diameter nanotubes. No such enhancement was observed upon encapsulation in hydrothermally synthesized nanotubes. In addition to this, the thermal stability of myoglobin was found to be enhanced upon confinement inside 200 nm diameter TiO 2 nanotubes.

The American Cancer Society predicts that 1,665,540 people will be diagnosed with cancer, and 585,720 people will die from cancer in 2014. One of the most common types of cancer in the United States is skin cancer. Melanoma alone is predicted to account for 10,000 of the cancer related deaths in 2014. As a highly mobile and aggressive form of cancer, melanoma is difficult to fight once it has metastasized through the body. Early detection in such varieties of cancer is critical in improving survival rates in afflicted patients. Present methods of detection rely on visual examination of suspicious regions of tissue via various forms of biopsies. Accurate assessment of cancerous cells via this method are subjective, and often unreliable in the early stages of cancer formation when only few cancer cells are forming. With fewer cancer cells, it is less likely that a cancer cell will appear in a biopsied tissue. This leads to a lower detection rate, even when cancer is present. This lack of detection when cancer is in fact present is referred to as a false negative. False negatives can have a highly detrimental effect on treating the cancer as soon as possible. More accurate methods of detecting cancer in early stages, in a nonsubjective form would alleviate these problems. A proposed alternative to visual examination of biopsied legions is to utilize fluorescent nanocrystalline biomarker constructs to directly attach to the abnormal markers found on cancerous tissues. Quantum dots (QDs) are hydrophobic nanoscale crystals composed of semiconducting materials which fluoresce when exposed to specific wavelengths of radiation, most commonly in the form of an ultraviolet light source. The QD constructs generated were composed of cadmium-selenium (CdSe) cores encapsulated with zinc-sulfide (ZnS) shells. These QDs were then encapsulated with phospholipids in an effort to create a hydrophilic particle which could interact with polar fluids as found within the human body. The goal of this thesis is to develop a method for the solubilization, encapsulation, and initial functionalization of CdSe/ZnS QDs. The first stage of this thesis focused on the generation of CdSe/ZnS QDs and the fluorescence differences between unshelled and shelled QDs. The second stage focused on utilizing the shelled QDs to generate hydrophilic constructs by utilizing phospholipids to bind with the QDs. Analysis via spectroscopy was performed in an effort to characterize the difference in QDs both prior to and after the encapsulation process. The method generated provides insight on fluorescence trends and the encapsulation of QDs in polar substances. Future research focusing on the repeatability of the process, introducing the QD constructs to a biological material, and eventual interaction with cancer cells are the next steps in generating a new technique to target and reveal skin cancer cells in the earliest possible stages without using a biopsy.