Alors que la découverte de matériaux conducteurs de faible dimension fait progresser la mi- niaturisation des composants électroniques, les transistors à effet de champ (FET) peuvent désormais incorporer des éléments à molécule unique comme canal ou grille. Ces petites architectures permettent, entre autres, l’étude de molécules uniques, notamment par l’ob- servation de leur dynamique de repliement-dépliement ou de liaison. Ces études ont été principalement réalisées avec des transistors à effet de champ à base de matériaux unidimen- sionnels (1D) tels que les nanotubes de carbone (CNT) ou les nanofils de silicium. Du fait de leur dimensionnalité réduite, ces matériaux offrent un bon contrôle de leur interaction avec les molécules 0D, et donc de leur intégration au circuit. Cependant, ces matériaux 1D présentent des problèmes de reproductibilité et de mise à l’échelle, du fait qu’ils sont difficiles à croître et/ou à assembler dans les dispositifs FET. Cette thèse s’intéresse à l’utilisation d’un matériau carboné à deux dimensions, le gra- phène, comme alternative pour la fabrication de dispositifs pour l’étude de dynamiques de molécules uniques. En effet, le graphène est un matériau à deux dimensions composé d’un ré- seau hexagonal d’atomes de carbone, avec une excellente conductivité électrique ainsi qu’une chimie à base de carbone permettant l’ancrage de molécules biologiques à sa surface, ce qui en fait un candidat de choix pour la détection électrique de molécules individuelles. Sa di- mensionnalité est aussi compatible avec des procédés de microfabrication à grande échelle, ce qui offre la possibilité d’études statistiques sur de grands nombres de dispositifs. Ainsi, la détection de molécules biologiques utilisant des transistors à effet de champs à base de graphène (GFET) a connu un développement et un engouement important au cours de la dernière décennie, mais plusieurs aspects restent à résoudre, notamment la mise à l’échelle de la fabrication, le contrôle de la chimie de fonctionnalisation, et la miniaturisation du canal à l’échelle de la molécule unique. Dans cette thèse, des contributions sur ces trois aspects sont présentées. Premièrement, je décris une méthode de mise à l’échelle du transfert de graphène dans une optique d’indus- trialisation, par la conception et l’implémentation d’un montage de transfert de graphène permettant l’automatisation et l’augmentation du rendement de la fabrication de GFET. Je m’intéresse ensuite à la fonctionnalisation des dispositifs de graphène avec une molécule d’ancrage communément utilisée dans le cas des biodétecteurs basés sur des GFET, afin de révéler les cinétiques associées à l’adsorption et à l’accumulation de la molécule à la surface du graphène. Enfin le dernier chapitre décrit la conception d’une architecture de GFET pour l’accueil d’une molécule unique d’ADN, basée sur des nanoconstrictions mises en place dans le canal de graphène. Ces constrictions ont été obtenues à l’aide de la lithographie par faisceau d’électrons (EBL) et gravure ionique réactive profonde (DRIE), qui nous permet de modeler des structures à haute résolution de quelques dizaines de nanomètres dans le canal de graphène. Des nanopuits perpendiculaires à la constriction sont par la suite ouverts dans de la résine, favorisant le confinement de la chimie d’immobilisation de la molécule unique en un seul point. J’explore ensuite la liaison d’un brin unique d’ADN sur la nanoconstriction, et l’étude dynamique de son repliement. Cette thèse présente donc des résultats innovants en termes d’architectures et de procédés de mise à l’échelle de GFET à des fins de biodétection. / With the discovery of low-dimensional conductive materials advancing the miniaturization of electronic components, field-effect transistors (FET) can now incorporate single-molecule elements as a channel or gate. Among their applications, these small architectures allow single-molecule studies, for instance by observing their folding-unfolding or binding dy- namics. These studies were mainly carried out with field-effect transistors based on one- dimensional (1D) materials such as carbon nanotubes (CNT) or silicon nanowires (SiNW). Due to their reduced dimensionality, these materials offer good control on their interaction with 0D molecules, and therefore of their integration into the circuit. However, these 1D materials present reproducibility and scaling issues, due to the fact that they are difficult to grow and/or assemble in FET devices. This thesis focuses on the use of a two-dimensional carbon-based material, graphene, as an alternative for the fabrication of devices for studying the dynamics of single molecules. Graphene is a hexagonal network of carbon atoms that offers an excellent electrical conduc- tivity as well as a carbon-based chemistry for anchoring biological molecules on its surface, this makes it a prime candidate for the electrical detection of individual molecules. Above all, its dimensionality is compatible with large-scale microfabrication processes, which offer the possibility of statistical studies on a large number of devices. Thus, the detection of biological molecules using graphene-based field-effect transistors (GFET) has experienced significant development over the past decade, but several aspects remain to be resolved, including scale- up of the manufacturing, control of the functionalization chemistry, and miniaturization of the channel at the single molecule scale. In this thesis, I present contributions on these three aspects. First, I describe a method for scaling up graphene transfer in an industrialization perspective, by designing and implementing a graphene transfer setup allowing automation for increasing the yield of GFET fabrication. I then focus on the functionalization dynamics of graphene devices with an anchor molecule named PBASE (1-Pyrenebutyric acid N-hydroxysuccinimide ester) commonly used in the case of GFET-based biosensors, which reveals the adsorption and accumulation kinetics of the molecule on the graphene surface. Finally, I describe the design of a GFET architecture based on nanoconstrictions implemented in the graphene channel, designed to host a single molecule. These constrictions were obtained using electron beam lithography (EBL) and deep reactive ion etching (DRIE), which allows the modeling of high-resolution features of a few nanometers in the graphene channel. Nanowells were opened in the resin perpendicular to the constriction, promoting single-point, single-molecule chemistry. I then explore the immobilization of a single strand of DNA on nanoconstriction, and the dynamic study of its folding. This thesis therefore presents innovative results in terms of architectures and scaled implementation processes of GFET for biodetection purposes.

<p>Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been established as a powerful tool for qualitative and quantitative analysis of biomolecules. However, mass spectrometric analysis of biomolecules is often limited by poor ionization efficiency of analyte for sensitive detection and limited fragmentation for structural characterization. Over the years, various solution phase as well as gas-phase derivatization techniques, have been coupled with MS to increase the ionization efficiency and facilitate the formation of structural informative fragment ions. The research presented in this dissertation falls into two major parts; focusing on method development and application of radical chemistry for enhanced biomolecule analysis on an ESI-MS/MS platform. In the first part, a method of rapid charge tagging of neutral lipids (e.g. sterols, glycerides) with a thiol radical-based charge tag is developed, followed by comprehensive analysis via ESI-MS/MS without the use of a chromatographic separation (shotgun lipidomics). This charge tagging is performed in an easily constructible fused silica capillary-based microflow photo-reactor which is relatively low in cost and requires no instrument modifications. This method significantly enhances the ionization efficiency of the neutral lipids for sensitive MS detection (pM range). This method can be applied to the small volume of biological complex samples (e.g. 1 µL plasma) and doesn’t require extensive sample pretreatment procedure (analysis time of 2 min vs. traditional >60 min on GC-MS and HPLC-MS systems). Furthermore, the derivatized neutral lipids can also be fragmented via soft collision-induced dissociation to obtain fatty acyl chain composition of the neutral lipids (sterol esters, diacylglycerols, triacylglycerols, etc.) for structural characterization. This can especially be useful for determination for fatty acyl compositional isomers in neutral lipids for analysis related to biomarker detection. The characteristic fragmentation pattern of tagged neutral lipids has also been utilized for quantitation of lipids from biological mixture samples. Initial application of this method has shown alteration in the concentration of diacylglycerol lipid species in clinical samples of Type 2 Diabetes Mellitus patients, suggesting the potential of understanding the biological roles of such lipids in insulin resistance. </p> <p>In the second part, a unique approach of radical-induced disulfide bond cleavage in peptides and proteins is demonstrated. Using 254 nm UV emission, acetone was used as a photoinitiator to initiate secondary radical formation i.e. hydroxyalkyl radical, from alcohol co-solvents used for electrospray. These radicals can then be used to efficiently cleave the disulfide bonds (R-S-S-R) in peptide/proteins to give reduced reaction products (RSH) at the cleavage site. Upon soft collision-induced dissociation, the reduced product gave abundant <i>b-</i> and <i>y-</i> type fragment ions for complete or enhanced sequence coverage as compared to intact disulfide-linked peptides and proteins. With the use of a simple microflow photo-reactor, this radical based approach can also be coupled with infusion ESI-MS/MS for a rapid online-based peptide and protein analysis. The yield for disulfide bond reduction was almost 100% within less than 5 s of UV irradiation. Furthermore, by adjusting the UV irradiance time, different degrees of partial reduction could be achieved, which greatly facilitated the disulfide linkage mapping in peptides and proteins with multiple disulfide bonds. This method has been incorporated with both bottom-up and top-down approach for protein analysis for unraveling the molecular complexity, quantifying and deep sequencing of disulfide-linked proteins.</p>

Le présent travail de thèse repose sur la conception d'un système miniaturisé de type biopuce capable d'assurer la capture et le relargage contrôlé de différentes populations des cellules sanguines (e.g. lymphocytes). Ce projet a pour objectif la construction d'un outil potentiel de recherche dans le domaine de l'immunologie ainsi que du diagnostic qui permettrait non seulement de réaliser des essais à partir d'une faible quantité d'échantillon, mais aussi de réduire le temps d'analyse. L'approche consiste plus précisément en la fabrication d'une matrice d'oligonucléotides et l'immobilisation de cellules via une molécule hybride composée d'un anticorps IgG couplé à une séquence d'oligonucléotide complémentaire. La synthèse du produit conjugué est mise en place et conduit à l'assemblage functionnel sur biopuce. Une fois les cellules spécifiquement capturées sur la surface, deux voies de rélargage contrôlé sont explorées. Ainsi, les lymphocytes sont libérées de façon contrôlée et séquentielle par clivage enzymatique d'ADN ou alors par désorption physique possible grâce au chauffage localisé. La détection se fait en temps réel par l'imagerie de la résonance plasmonique de surface (Surface Plasmon Resonance Imaging, SPRi) qui présente l'avantage de pouvoir suivre les phénomènes biomoléculaires en absence de marquage et d'apporter une réponse simultanée d'un échantillon biologique sur un grand nombre des sondes. Accessoirement, une approche instrumentale particulière nous permet d'observer les étapes de capture/relargage par microscopie optique classique. La construction de la biopuce permet également l'élargissement à plusieurs cibles et ouvre ainsi la voie à de nombreuses possibilités d'exploration en termes d'application pour l'analyse d'échantillons biologiques plus complexes tels que du sang. / This PhD thesis is devoted to conception of a miniaturized system of biochip type able to realize a controlled capture and release of different populations of the blood cells (e.g. lymphocytes). The main objective of the project is to create a potential tool of research, especially in the field of immunology, and medical diagnostics as well, that could perform short-time analyses by using a small sample amount. The approach relies more precisely on fabrication of a DNA matrix and further immobilization of cells through a hybrid molecule composed of an IgG antibody covalently coupled with short oligonucleotide sequence. Synthesis of the conjugated product is developed and demonstrates functional assembly on the micro-platform. Lymphocytes are specifically addressed onto biochip surface and once they are captured, two independent strategies of selective release are proposed. Therefore, immobilized cells are specifically detached either upon enzymatic cleavage of oligonucleotide substrate or physically desorbed by local heating and denaturation of double stranded DNA. The system makes use of Surface Plasmon Resonance Imaging (SPRi) to enable real time detection of different biomolecular phenomena in a label-free and high-throughput manner. Accessorily, a particular instrumental approach is developed in order to observe cell capture-release steps directly under optical microscopy. The biochip construction permits to extend its performance to many targets and may be further explored in terms of application to analysis of complex biological samples such as blood.

Cancer is the second leading cause of mortality in the United States and the World, therefore, early effective prevention, diagnosis, and therapy is needed. Estrogens play a major role in the initiation and progression of breast cancer. Elevated lifetime exposure to estrogens is associated with an increased risk of developing breast cancer. Estrogens through influencing mitochondria contribute to estrogen induced breast carcinogenesis; however, the exact mitochondrial mechanisms underlying the estrogen carcinogenic effect in breast tissue are not clearly understood. For this dissertation, the mitotoxic and cytotoxic effects of triphenylphosphonium cation (TPP) and Origanum majorana organic extract (OME) as well as PEGylated bioconjugate of OME with TPP (P-OME-TPP) against human breast epithelial and cancer cell lines was investigated. Initially, TPP, a lipophilic cation, was used to check whether an imbalance in mitochondrial bioenergetics, in part, may be responsible for estrogen induced growth of breast cancer. The results showed that exposure of estrogen-dependent MCF-7 cells to 17 β-estradiol (E2) induced the metabolic activity, proliferation, mitochondrial bioenergetics, DNA damage, and formation of cellular and mitochondrial reactive oxidant species (ROS). These E2-induced endpoints were inhibited by co-treatment with TPP, indicating mitochondrial mechanisms, in part, may contribute to the development of breast cancer. Furthermore, O. majorana, widely used in the Middle East as a culinary aromatic medicinal herb, has been shown to possess an extensive range of biological activity including antioxidant, anti-inflammatory, and anti-tumor growth effects. Interestingly, the anticancer potential of O. majorana against breast cancer remains largely unexplored; therefore, the anticancer effect of O. majorana on breast cell lines was investigated. The results showed that E2-induced metabolic activity and growth were inhibited by OME in MCF-7 cells. The results also demonstrated that synthesized P-OME-TPP conjugate, compared to OME, was far more effective in exerting its cytotoxic effect through the inhibition of growth and mitochondrial metabolic activity in both highly metastatic, triple negative MDA-MB-231 and estrogen-dependent MCF-7 breast cancer cells. Altogether, these findings offer a new perspective on the utility of mitochondria-targeted lipophilic TPP cation and the potential of O. majorana extract to be developed as a new therapy against breast tumors.

Ce mémoire présente une étude expérimentale de la fragmentation en phase gazeuse des biomolécules, adénine (H5C5N5) et porphyrine FeTPPCl (C44H28N4FeCl), induite par collision avec des ions à basse énergie. La distribution de population pour chaque voie de dissociation a été mesurée en fonction de l'énergie d'excitation des ions moléculaires parents avec la méthode CIDEC (Collision Induced Dissociation under Energy Control). Dans les collisions entre Cl+ à 3keV et adénine (Ade), le schéma de fragmentation de Ade2+ est dominée par la perte de H2CN+ et les émissions successives de HCN. La distribution de l'énergie des Ade2+ parents confirme la dynamique des émissions successives. Une voie de dissociation spécifique, à savoir l'émission successive de H2CN+ et HC2N2 est observée. Les schémas de fragmentation des ions moléculaires FeTPPCl1+, 2+, 3+ sont étudiés dans des collisions avec Kr8+ à 80 keV. Il est constaté qu’indépendante de l'état de charge initiale de FeTPPClr+ (r=1, 2, 3), la perte de Cl0 constitue la première étape de la chaîne de dissociation, tandis que l’état de charge initiale des molécules joue un rôle important dans les étapes suivantes de la dissociation. Dans les collisions avec H+ et F+ à 3keV, dû à un effet de fenêtre de réaction dans les processus de production d’ions négatifs, des schémas de fragmentation très différents sont observés pour FeTPPCl2+. Grâce à la mesure de l’énergie interne des molécules parents, la perte de nH2 est observée et analysée. De plus, le rendement de production d'ions négatifs, mesuré à environ 1% dans des collisions F2+-Ade à 30 keV, est étudié dans ce travail en utilisant une nouvelle approche expérimentale. / In this work, the Collision Induced Dissociation under Energy Control method was extended to study the fragmentation of gas-phase biomolecules adenine (H5C5N5) and porphyrin FeTPPCl (C44H28N4FeCl). The population distribution for each dissociation channel has been experimentally determined as a function of the excitation energy of the parent molecular ions at a well-determined initial charge state. In collisions between Cl+ and adenine (Ade) at 3keV, the fragmentation pattern of Ade2+ is dominated by the loss of H2CN+ and the successive emission of HCN. The energy distribution of the parent dications confirms the successive emission dynamics. A specific decay channel is observed, i.e., the emission of a charged H2CN+ followed by the emission of HC2N2. In Kr8+-FeTPPCl collisions at 80keV, parent ions FeTPPCl1+,2+,3+ are observed, along with the corresponding decay patterns. It is found that in the first step the dominant low-energy-cost decay channel is the emission of Cl0 independent of the initial charge state of FeTPPClr+ (r=1-3). For the resulted dication FeTPP2+, the dominant fragmentation channel is the neutral evaporation; for the trication however, the dominant fragmentation channel is the asymmetrical fission. In the case of H+ and F+ impact at 3keV, due to the different reaction windows opened in the two collision systems, different fragmentation patterns are observed. Furthermore, nH2 loss processes are observed. Additionally, the production yield of the negative ion emerged in F2+-Ade collision at 30keV is measured to be about 1% using a new experimental approach.

This thesis deals with the research work carried out for the development of novel applications by integrating biomolecules with various nanostructures. The thesis is organized as follows: Chapter 1 reviews the properties of nanomaterials which are important to consider while developing them for various biological and other applications. It discusses the factors which affect the cytotoxicity of nanocrystals towards living cells, photocatalytic mechanisms of nanocrystals that work behind the inactivation of bacterial cells and gas sensing properties of nanocrystals. It also mentions about the integration of biomolecules with nanomaterials which is useful for the development of biosensors, materials that are presently used for fabricating biosensors and the challenges associated with designing successful biosensors. Chapter 2 presents the antibacterial and anticancer properties of ZnO/Ag nanohybids. In this study a simple route to synthesize ZnO/Ag nanohybrids by microwave synthesis has been established where ZnO/Ag nanohybrids have shown synergistic cytotoxicity towards mammalian cells. The observed synergism in the cytotoxicity of ZnO/Ag nanohybrids could lead to the development of low dose therapeutics for cancer treatment. Chapter 3 presents photocatalytic inactivation of bacterial cells by pentavalent bismuthates class of materials. AgBiO3 which was obtained from KBiO3 by ion-exchange method was investigated for its photocatalytic inactivation properties towards E.coli and S.aureus cells under dark and UV illumination conditions. Chapter 4 presents the integration of DNA molecules with ZnO nanorods for the observation of Mott-Gurney characteristics. In this study, ZnO nanorods were synthesized hydrothermally and were characterized by TEM and XRD analysis. DNA molecules were immobilized over ZnO nanorods which were confirmed by UV-Vis spectroscopy and confocal florescence microscopy. Solution processed devices were fabricated by using these DNA immobilized nanostructures and I-V characteristics of these devices were taken in dark and under illumination conditions at different wavelengths of light at fixed intensity. Interestingly, Mott-Gurney law was observed in the I-V characteristics of the devices fabricated using DNA immobilized ZnO nanorods. Chapter 5 presents the chemical synthesis of molecular scale ultrathin Au nanowires. These nanostructures were then used for fabricating electronic biosensors. In this study, the devices were fabricated over Au nanowires by e-beam lithography and a methodology to functionalize Au nanowires and then characterize them by florescence microscopy as well as AFM has been established. The fabricated biosensors were employed for the label free, electrical detection of DNA hybridization process. Chapter 6 presents a simple, cost effective and solution processed route to fabricate devices using ultrathin Au nanowires. The devices were then used for sensing ethanol, H2 and NH3. An important property of these devices is that they can sense these gases at room temperature which reduce their operation cost and makes them desirable to use under explosive conditions.

Title: Multicomponent plasma polymers with spatially controlled properties Author: MSc. Pavel Pleskunov Department / Institute: Department of Macromolecular Physics/Charles University Supervisor of the doctoral thesis: Prof. Ing. Andrey Shukurov, PhD, Department of Macromolecular Physics / Charles University Abstract: Mixing of two (or more) polymers often leads to phase separation and to the formation of nanoscale architecture, which can be highly attractive in various applications including controllable drug delivery, fabrication of separation and solid electrolyte membranes, gas storage, etc. Different wet-chemistry techniques already exist to produce nanophase-separated polymers; however, capturing the resultant polymeric structure in a predictable manner remains a challenging task. In this thesis, a low-temperature plasma-based strategy is investigated for the production of multicomponent thin films of plasma polymers with spatially discriminated nanoscale domains. Gas aggregation cluster source is used for the fabrication of nanoparticles of plasma polymerized acrylic acid, whereas Plasma-Assisted Vapor Phase Deposition is used for the deposition of thin films of poly(ethylene oxide) plasma polymer. Embedding of nanoparticles into matrices of thermodynamically incompatible plasma polymer as well as...

Membrane filtration processes are widely utilized across different industrial sectors for biological and environmental separations. Examples of the former are sterile filtration and protein fractionation via microfiltration (MF) and ultrafiltration (UF) while drinking water treatment, tertiary treatment of wastewater, water reuse and desalination via MF, UF, nanofiltration (NF) and reverse-osmosis (RO) are examples of the latter. A common misconception is that the performance of membrane separation is solely dependent on the membrane pore size, whereas a multitude of parameters including solution conditions, solute concentration, presence of specific ions, hydrodynamic conditions, membrane structure and surface properties can significantly influence the separation performance and the membrane’s fouling propensity. The conventional approach for studying filtration performance is to use a single lab- or pilot-scale module and perform numerous experiments in a sequential manner which is both time-consuming and requires large amounts of material. Alternatively, high-throughput (HT) techniques, defined as the miniaturized version of conventional unit operations which allow for multiple experiments to be run in parallel and require a small amount of sample, can be employed. There is a growing interest in the use of HT techniques to speed up the testing and optimization of membrane-based separations. In this work, different HT screening approaches are developed and utilized for the evaluation and optimization of filtration performance using flat-sheet and hollow-fiber (HF) membranes used in biological and environmental separations. The effects of various process factors were evaluated on the separation of different biomolecules by combining a HT filtration method using flat-sheet UF membranes and design-of-experiments methods. Additionally, a novel HT platform was introduced for multi-modal (constant transmembrane pressure vs. constant flux) testing of flat-sheet membranes used in bio-separations. Furthermore, the first-ever HT modules for parallel testing of HF membranes were developed for rapid fouling tests as well as extended filtration evaluation experiments. The usefulness of the modules was demonstrated by evaluating the filtration performance of different foulants under various operating conditions as well as running surface modification experiments. The techniques described herein can be employed for rapid determination of the optimal combination of conditions that result in the best filtration performance for different membrane separation applications and thus eliminate the need to perform numerous conventional lab-scale tests. Overall, more than 250 filtration tests and 350 hydraulic permeability measurements were performed and analyzed using the HT platforms developed in this thesis. / Thesis / Doctor of Philosophy (PhD) / Membrane filtration is widely used as a key separation process in different industries. For example, microfiltration (MF) and ultrafiltration (UF) are used for sterilization and purification of bio-products. Furthermore, MF, UF and reverse-osmosis (RO) are used for drinking water and wastewater treatment. A common misconception is that membrane filtration is a process solely based on the pore size of the membrane whereas numerous factors can significantly affect the performance. Conventionally, a large number of lab- or full-scale experiments are performed to find the optimum operating conditions for each filtration process. High-throughput (HT) techniques are powerful methods to accelerate the pace of process optimization—they allow for multiple experiments to be run in parallel and require smaller amounts of sample. This thesis focuses on the development of different HT techniques that require a minimal amount of sample for parallel testing and optimization of membrane filtration processes with applications in environmental and biological separations. The introduced techniques can reduce the amount of sample used in each test between 10-50 times and accelerate process development and optimization by running parallel tests.