The aim of my PhD research was to develop and establish techniques for surface functionalization of nanoparticles, which can be employed to study the dynamics, function and activity of recombinantly expressed as well as endogenous proteins inside living cells. A prerequisite to achieve this goal was the ability to bio-functionalize nanoparticles with proteins in the cytoplasm of living cells. The HaloTag technology was utilized for generic site-specific targeting of nanoparticles to proteins. Fast and efficient targeting of nanoparticles to proteins was then achieved by using an engineered clickHTL exhibiting fast reactivity towards the HaloTag-enzyme. Application of this approach to track individual proteins in the outer membrane of mitochondria revealed that the physicochemical properties of the nanoparticles biased the mobility of the targeted proteins. To circumvent this, a model nanoparticle was systematically engineered in order to identify physicochemical properties that are important for tracking intracellular membrane proteins without affecting their diffusion dynamics. Nanoparticles exhibiting stealth properties were finally obtained upon densely coating the nanoparticle surface with PEG2k. These particles were mono-functionalization with clickHTL, to ensure labeling in a 1:1 stoichiometry, and could be successfully used for unbiased tracking of individual membrane proteins. Beyond the observation of proteins, generic approaches that allow intracellular manipulation and probing of protein activities are desired. To this end, 500 nm superparamagnetic nanoparticles were used as mobile nanoscopic hotspots self-assebled into active signaling platforms. Inside living cells, precise and accurate manipulation of endogeneous Rac1 activity was possible at different subcellular locations and over extended time periods. These experiments demonstrated that Rac1 signaling is dependent on the subcellular-context by spatial isolation of distinct signaling pathways. Furthermore, these MNPs provided well defined platforms for selective spectroscopy in order to quantify bait-prey protein interactions in the cytoplasm as was demonstrated by the interaction of cdc42 and N-WASP.

Spintronics is a rapidly growing research field due to scalability, integrablility within existing VLSI architecture, significantly reduced switching energy and latency while maintaining stable bit orientation (Spin-up, Spin-down). For the first time sub-5nm Spin Transfer Torque –Magnetic Tunneling Junctions (STT-MTJ) were investigated utilizing various Integrated Circuit (IC) fabrication techniques to evaluate novel concepts in logic switches. Tunneling Magnetoresistance (TMR) was measured in STT-MTJ stacks of Ta/CoFeB/MgO/CoFeB/Ta with differing diameter ferrimagnetic CoFe2O4 nanoparticles (10nm, 4nm and 2nm) embedded in the MgO layer. MR was detected in the 2nm and 4nm particle devices and demonstrated evidence of single electron transport. Tri-layer STT-MTJ devices were fabricated using a thin film stack of Ta/Ru/Ta/CoFeB(M1)/MgO/CoFeB(M2)/MgO/CoFeB(M3)/Ta. The overall diameter of the stack was reduced to sub-20nm using Focused Ion Beam (FIB) to mill away extra material. The coercivities of the ferrimagnetic CoFeB layers were modified during thin film deposition by altering sputter conditions. Field Applied- Magnetic Force Microscopy (FA-MFM) was used to detect four different magnetic intensities corresponding to three discreet resistances in the singly addressed device, making this architecture a candidate for neuromorphic computational applications. Lastly a lithographic-less architecture was developed to mass fabricate and electo-mechanically probe multi-layered, single point, sub-5nm particle based STT-MTJ devices using off-the-shelf anodized nanoporous alumina. Once fabricated, the devices were probed to measure their IV characteristics and magnetoresistance (MR). The unprecedented MR changes on the order of 50,000% at room temperature suggest quantum mechanical behavior.

Indiana University-Purdue University Indianapolis (IUPUI) / Nanoparticles (NPs) are an emerging technology in biomedical engineering with opportunities in diagnostics, imaging, and drug delivery. NPs can be prepared from a wide range of organic and/or inorganic materials. They can be fabricated to exhibit different characteristics for biomedical applications. The goal of this thesis was to develop NPs with tunable surface properties for selective cell targeting. Specifically, polyelectrolyte complexes composed of heparin (Hep, a growth factor binding glycosaminoglycan) and poly-L-lysine (PLL, a homopolymeric lysine) were prepared via a pulse sonication method. The Hep/PLL core NPs were further layered with additional Hep, tetrazine (Tz) modified Hep, or dextran sulfate (DS). The addition of Tz handle on Hep backbone permitted easy modification of NP surface with norbornene (NB) modified motifs/ligands, including inert poly(ethylene glycol) (PEG), cell adhesive peptides (e.g., RGD), and/or fluorescent marker. Both Hep and DS coated NPs could be readily internalized by J774A.1 monocytes/macrophages, whereas PEGylated NPs effectively reduced cellular uptake/recognition. The versatility of this NP system was further demonstrated by laying DS on the Hep/PLL NP surface. DS-coated NPs were recognized by J774A.1 cells more effectively. Furthermore, DS-layered NPs seemed to reduce IL-10 production on a per cell basis, suggesting that these NPs could be used to alter polarization of macrophages.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20672号 / 医博第4282号 / 新制||医||1024(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 妹尾 浩, 教授 野田 亮, 教授 岩田 想 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21442号 / 理博第4435号 / 新制||理||1637(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 北川 宏, 教授 竹腰 清乃理, 教授 吉村 一良 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Oligothiophenes are of increasing interest in organic based electronic devices in part due to their high electron and hole mobilities. In an organic photovoltaic (OPV) device, the electronic properties of oligothiophenes make them advantageous as charge transfer junctions. To serve as charge transfer junctions, oligothiophenes must be functionalized to bind to the donor and acceptor parts of the device. The donor and acceptor parts are different materials and the synthesis of asymmetric oligothiophenes is of great interest. Previous researchers in our lab synthesized four asymmetric oligothiophenes, two with two thiophene subunits and two with four. Each set of oligothiophenes contained a pair of constitutional isomers. Here we report the synthesis of another asymmetric oligothiophene, one with three thiophene subunits. This compound is functionalized with bipyridine to bind Ru(bpy)22+ and with phosphonic acid moieties to bind CdSe nanoparticles. The synthesis was carried out by bonding a phosphonic acid moiety to bithiophene and bipyridine to thiophene and then coupling the phosphate-bithiophene and thiophene-bipyridine. Standard Stille couplings were used for carbon-carbon bond formation. The resulting compounds have complex NMR spectra and overlapping Ru MLCT and π-π* transitions at 450 nm with molar extinction coefficient on the order of 3 x 105 M-1 cm-1. The thiophene fluorescence is quenched by Ru(bpy)22+. These optical properties compare closely with the previous compounds synthesized. Solar cells occupy significant attention in the media, politics and science for their promise of continual pollution-free energy. Quantum dots, metal complexes and organic compounds are all under research as viable replacements for expensive silicon solar cells. To test the efficacy of a light harvesting compound before constructing a solar cell, a model system is constructed to show electron transfer from the light harvester into an electron acceptor. We synthesized oligothiophenes and oligothiophene-ruthenium complexes and tested their ability to act as sensitizers and charge transfer junctions. To do this, they were bonded to CdSe nanoparticles and their optical properties were measured. Steady-state photoluminescence and time correlated single photon counting were used to observe the effects on fluorescence and fluorescence lifetime of the CdSe-oligothiophene and CdSe-oligothiophene-ruthenium complexes before and after binding. It was found that CdSe fluorescence was quenched when bound to an oligothiophene ruthenium complex, and that the fluorescence of the oligothiophene was quenched when bound to CdSe in the absence of ruthenium. The fluorescence lifetimes of the quenched species were shortened.

The billion dollar pharmaceutical research and development pipeline suffers greatly from high attrition rates of novel therapeutic compounds within pre-clinical and clinical trials. Poor bioavailability in many new drugs, originating in the various methodologies of high throughput screening, may explain part of these growing failure rates. One interpretation of this phenomenon relies on bioavailability's correlation with aqueous solubility; much modern processing allows chemicals to fully develop without touching water, yielding upwards of 90% of new chemical entities practically insoluble in aqueous media. Thus, one approach to alleviating bioavailability and potentially clinical attrition rates necessitates augmented aqueous solubility. The amorphous nanoparticle presents the largest boost in aqueous solubility of a chemical through processing alone. In this contribution, we propose electrospray as a novel, competitive candidate to produce pharmaceutical amorphous nanoparticles with the intent of augmenting solubility. Electrospray represents an idyllic nominee for three reasons: repeatability, flexibility, and scalability. Electrospray offers low batch to batch variation with less than 30% relative standard deviation between various droplets. This triumphs over the several orders of magnitude in variation in pneumatic sprays. Electrospray's flexibility draws from its ability to attain diameters over several orders of magnitude, ranging from hundreds of microns to several nanometers; in this contribution droplets are produced between 500 nm and 1[micro]m. Finally, electrospray displays scalability to any industrial requirement; though a single nozzle operates at mere microliters per hour, a single multiplexed array of emitters may increase this throughput by several orders of magnitude. This exploration, utilizing Indomethacin as a model low solubility chemical, verifies electrospray as a compatible processing tool for the pharmaceutical industry. Scanning electron microscopy coupled with the image analysis software ImageJ gleans the size and shape of emitted (and dried) particles. Amorphicity verification of particles employs grazing angle x-ray diffraction. Finally, ultraviolet and visual spectrum spectroscopy evaluates the solubility advantage of particles.

Autophagy is an essential quality control process in which proteins and organelles are degraded. In this work, we first extended our understanding of autophagic degradation in disease by investigating the use of acidic nanoparticles to restore autophagic flux in a neurotoxic model of Parkinson Disease (PD). Normal autophagic degradation follows two key steps. First, material is engulfed to form a double-membraned autophagosome. Next, autophagosomes fuse with an acidic lysosome to degrade the inner membrane contents. Insufficient lysosomal acidity results in autophagic flux arrest, and in PC-12 cells, we characterized the use of polymeric nanoparticles as a tool to restore lysosomal acidity and rescue autophagic flux in PC-12 cells. Specifically, in an MPP+ model of neurotoxicity, we demonstrated that formulations of poly(lactic-co-glycolic acid) nanoparticles (PLGA) improved lysosomal acidity, autophagic flux, and cell health significantly, but is likely limited in efficacy by polymer degradation rate. To improve upon this, we developed a new acidic nanoparticle formulated with a novel polymer backbone (termed acNPs), engineered to degrade within lysosomes and release tetrafluorosuccinic acid, a highly potent acid (pKa ~1.6). On the benchtop, these engineered nanoparticles demonstrated both colloidal instability and acid release within a weakly acidic environment (pH 6.0) similar to a diseased lysosome but not at a neutral pH of 7.4. In cells, acNPs effectively decreased lysosomal pH within disease lysosomes, thereby restoring autophagic flux and mitochondrial activity in PC-12 cells. Encouragingly, we also were able to show efficacy of acNPs in 2D and 3D models of the human midbrain. acNPs readily trafficked within the lysosomes of cells in 2D midbrain cultures and 3D midbrain organoids. Similar to PC-12 cells, when we challenged these cells in a model of neurotoxicity, we observed restoration of viability in human organoids following acNP treatment. Next, we addressed some current challenges regarding the quantification of autophagy within cells. We repurposed measures of economic income inequality to quantify the spatial dispersion of LC3 signal intensity in a starvation model of autophagy, and then compared these measures to other image-based measurements based on their ability to represent LC3-II levels, a robust protein marker of the autophagosome. Our analysis showed these indices outperformed all other generated measurements, including the current standard of autophagy research, LC3 puncta counting. Additionally, we also explored the linear decomposition properties of the generalized entropy index and found it a facile way to evaluate autophagic flux within 3D imaging datasets of multicellular systems. Specifically, we revealed a differential response to nutrient depravation between neurons and astrocytes. Finally, we translated this paradigm to a high throughput cell assay where we demonstrated EC50 and IC50 curves, produced from datasets acquired through both confocal and automated widefield fluorescence microscopy. Our results agree with standard cell assays.

Interprotein electron transfer (ET) is crucial for natural energy conversion and a fundamental reaction in the pursuit of understanding the broader problem of proteinprotein interactions and reactivity. Simplifying the complicated nature of these natural systems has driven development of biomimetic approaches. Functionalized gold nanoparticles offer simplified, tunable surfaces that can serve as a proxy to study the reactivity and dynamics of proteins. Amino-acid functionalized gold nanoparticles (Au-TX) served as a complementary partner to cytochrome c (Cyt c) and catalyzed its ET reactivity without altering the native structure. Redox mediator and EPR experiments confirmed that the redox potential and coordination environment of the heme were unaltered. Varying the functionality of Au-TX under limiting redox reagent concentrations resulted in distinct ET reactivity. These conditions reflected the collision of a small redox reagent with the Cyt c/Au-TX adduct, introducing the possibility of Cyt c/Au-TX dynamics to modulate ET. Under high ionic strength conditions, the rate enhancement ranged from 0.0870 " 1011 for Cyt c/Au-TAsp to 1.95 " 1011 M-1 s-1 for Cyt c/Au-TPhe. Au-TAsp binds to a larger surface of the front face of Cyt c than Au-TPhe, likely reducing heme access and resulting in attenuated ET reactivity.Site-directed spin-labeling characterized the dynamic interactions and motion of Cyt c with Au-TX. Several mutants of Cyt c were utilized to extract information about the different dynamics of the Cyt c/Au-TPhe and Cyt c/Au-TAsp systems. Cyt c appeared to have a highly dynamic binding interaction with the surface of Au-TPhe while binding to Au-TAsp resulted in a more rigid interface, particularly at the heme crevice. The dynamic interaction of Cyt c/Au-TX at the heme crevice could promote a gated ET mechanism between Cyt c and its redox partner. Thus, the reduced reactivity of Cyt c/Au-TAsp is likely a result of both slower global dynamics and more rigid binding near the heme crevice.

Nanoparticles are regarded as exciting new building blocks for functional materials due to their fascinating physical properties because of the nano-confinement. Organizing nanoparticles into ordered hierarchical structures are highly desired for constructing novel optical and electrical artificial materials that are different from their isolated state or thermodynamics random ensembles. My research integrates the surface chemistry of nanoparticles, interfacial assembly and lithography techniques to construct nanoparticle based functional structures. We designed and synthesized tailor-made ligands for gold, semiconductor and magnetic nanoparticle, to modulate the assembly process and collective properties of the assembled structures, by controlling the key parameters such as particle-interface interaction, dielectric environments and inter-particle coupling etc. Top-down technologies such as micro contact printing, photolithography and nanoimprint lithography are used to guide the assembly into arbitrarily predesigned structures for potential device applications.