Ce projet traite de la synthèse de copolymères en étoile amphiphiles à coeur -cyclodextrine et de leurs possibles interactions avec une membrane lipidique modèle en tant que nanopores artificiels. Dans un premier temps, la synthèse d’un amorceur multifonctionnel, per(2-O-méthyl-3,6-di-O-hydroxypropyl)--CD, a été réalisée et sa caractérisation par RMN 1H, 13C et spectrométrie de masse (ESI-MS) confirme sa structure. La polymérisation d’oxyde de butylène amorcée par ce dérivé de -cyclodextrine, en présence de base phosphazène, a alors été réalisée dans un deuxième temps et nous a permis de synthétiser des polymères en étoile à 14 branches hydrophobes, caractérisés par RMN (1H, 13C, DOSY) et chromatographie d’exclusion stérique. Ces derniers polymères hydrophobes sont couplés à leur tour à des chaînes polymères hydrophiles, poly(éthylène glycol) par méthode convergente (substitution nucléophile, chimie clic), ou polyglycidol par méthode divergente, et la caractérisation de l’architecture des copolymères résultants a été réalisée (RMN, CES). Enfin, parmi les différentes applications potentielles, l’aptitude de ces copolymères en étoile à former des nanopores artificiels a été testée par électrophysiologie. / The aim of this work is the synthesis of amphiphilic star copolymers based on -cyclodextrin and their possible interactions with model lipid bilayers, such as artificial nanopores. In a first step, the synthesis of multifunctional initiator, per(2-O-methyl-3,6-di-O-hydroxypropyl)--CD, was performed and its characterization by 1H, 13C NMR and ESI-mass spectrometry confirms itsstructure. The polymerization of butylene oxide initiated by -CD derivative, in presence of phosphazene base, was then performed and allowed us to synthesize hydrophobic 14-arm star polymers, characterizedby NMR (1H, 13C, DOSY) and size exclusion chromatography. Hydrophilic macromolecular chains (polyethylene glycol, polyglycidol) are coupled to those latter hydrophobic polymers, using ‘grafting onto’ and ‘grafting from’ methods, and the characterization of the resulting copolymer architecture was performed (NMR, SEC). Finally, among the different potential applications, the ability of the star copolymers to form artificial nanoporeswas evaluated by patch-clamp technique.

L'analyse électrique par nanopore est une technique relativement nouvelle permettant l'analyse de nanoparticules et de composés chimiques à l'échelle de la molécule unique. On utilise un trou nanométrique fait dans une membrane isolante délimitant deux électrolytes. On peut ainsi mesurer la résistance électrique de ce nanopore au cours du temps. Quand une particule d'intérêt s'approche du pore, la résistance électrique de celui-ci augmente de manière transitoire et on obtient ainsi une signature électrique liée à cette particule. Les applications de cette technique vont de la détection de virus jusqu'au séquençage de l'ADN ou d'autres polymères. Les nanopores solides sont une voie de développement de cette technique, démontrant une plus grande adaptabilité et robustesse que les nanopores protéiques, dont le développement est néanmoins plus avancé à ce jour. Cette thèse discute de l'intégration dans un dispositif microfluidique des puces contenant un nanopore solide ainsi que des traitement de surface nécessaires à la bonne utilisation de ces derniers. / Nanopore-based electrical analysis is a relatively new technique for the analysis of nanoparticles and chemical compounds at the single molecule scale. A nanometric pore is placed in an ultra-thin insulating membrane. We can then measure the electrical resistance of the pore. When a particle goes near the pore, this resistance increases transiently, thus yielding information on the passing nanoparticle. The applications of such a technique range from virus detection to DNA or other polymers sequencing. Solid-state nanopores are a growing competitor to the more developed proteic nanopores showing better adaptability and robustness. This thesis discuss the microfluidic integration of solid-state nanopores as well as the surface enhancement to permit their use.

Les glycosaminoglycanes (GAGs), des polysaccharides bio-actifs exprimés à la surface des cellules et dans la matrice extracellulaire, sont à l’origine d’un grand nombre de processus physiologiques et pathologiques tels le développement embryonnaire, la croissance cellulaire, l’homéostasie, etc. Parmi les biopolymères, ils offrent le plus grand potentiel d’information grâce à la variété de combinaisons et de modifications régio-sélectives des monosaccharides les constituant. Leur analyse structurale représente ainsi l’un des défis des glycosciences les plus difficiles à relever. De nouvelles approches basées sur la détection à l’échelle de la molécule unique permettent l’observation directe et la nano-manipulation de biomolécules. Principalement utilisées pour les acides nucléiques ou les protéines, ces approches ont rarement été appliquées à l’étude des polysaccharides. Nous présentons ici la détection à l'échelle de la molécule unique d’oligo-glycosaminoglycanes individuels confinés dans un nanopore protéique d’aérolysine et d’α-hémolysine. Nos résultats montrent la capacité de cette technique à discriminer les oligosaccharides d’acide hyaluronique selon leur degré de polymérisation, d’après la durée et la fréquence des blocages de courants. La preuve de la translocation a été montrée par spectrométrie de masse. Cette approche nous a permis de suivre la dépolymérisation enzymatique de l’acide hyaluronique et de déterminer ses paramètres cinétiques. D’autres oligosaccharides (l'héparine, le dermatane sulfate et le dextrane sulfate) ont été étudiés, présentant des signatures caractéristiques différentes, mettant en évidence des différences de structures et/ou conformations. / Glycosaminoglycans (GAGs) are bio-active polysaccharide expressed at the cell surface and in the extra-cellular matrix, which mediate cell-cell and cell-matrix interactions at the origin of a variety of physiological and pathological activities such as in embryonic development, cell growth, homeostasis, etc. Among all biopolymers, they offer the largest potential of information owing the incomparable variety of combinations and region-selective modifications of their building monosaccharides. The structural analysis of such complex carbohydrates is recognized as one of the most challenging task of glycosciences. New approaches based on single-molecule detection are currently arousing great interest in biology as it allows the direct observation and nano-manipulation of bio-molecules. Mainly applied to nucleic acids and proteins, these approaches have been not often used for the study of carbohydrates. We report here the detection of individual glycosaminoglycan oligosaccharides confined in aerolysin and α-hemolysin proteic nanopores. Our results show the capability of this new approach to discriminate hyaluronic acid (HA) oligosaccharides according to their polymerization degree based on the analysis of duration and frequency of the current blockades. This feature prompted us to apply this approach to the enzyme monitoring of the hyaluronidase-catalyzed depolymerization of HA and the determination of its kinetic parameters. Translocation has also been proved by mass spectrometry. Other oligosaccharides like heparin, dermatan sulfate and dextran sulfate, have also been studied, showing different characteristic “fingerprints”, due to structure and/or conformation differences.

La translocation, le passage d'une macromolécule à travers un pore inséré dans une membrane, est impliquée dans de nombreux processus biologiques. On peut citer comme exemple le transport d'ARN ou de protéines entre les composants de la cellule, et l'infection d'une cellule par le passage d'un ADN viral à travers la membrane cellulaire. Aujourd'hui la translocation est aussi la base d'applications technologiques, comme le fait d'utiliser les pores en tant que détecteurs pour le séquençage rapide de molécules ou en tant que filtre moléculaire. La compréhension du processus de translocation est importante à la fois d'un point de vue fondamental et pour la fabrication de nouveaux dispositifs de translocation à usage spécifique. Dans cette thèse, nous réalisons des expériences et des simulations informatiques pour étudier certains des effets les plus importants mis en jeu lors de la translocation.Nous utilisons des simulations informatiques avec un modèle à ``gros grain'' pour étudier qualitativement l'influence d'une interaction attractive entre les parois du pore et un polymère en train de transloquer. Nous montrons que la position de l'interaction influence la fréquence d'entrée et le temps de résidence du polymère dans le pore. La fréquence d'entrée est plus grande lorsque l'entrée du pore est attractive. Le comportement du temps de résidence avec la longueur du polymère est qualitativement et quantitativement affecté par la position de l'interaction dans le pore. Cependant, quelle que soit la position de l'interaction, nous observons que le temps de translocation augmente linéairement avec la longueur du polymère lorsque le polymère est plus long que le pore. Cette observation est qualitativement en accord avec des données expérimentales publiées.Lorsque la translocation est lente, la corrélation entre les mouvements des monomères confinés dans le pore peut jouer un rôle important. Cet effet n'a pas été pris en compte jusqu'à présent. Nous développons un nouveau modèle pour la translocation de polymères, inspiré par le processus d'exclusion asymétrique (ASEP process), qui permet d'étudier spécifiquement cet effet. Nous montrons que les mouvements corrélés des monomères confinés dans le pore génèrent un comportement du temps de résidence avec la longueur du polymère qui est qualitativement similaire à ce qui est habituellement interprété comme la présence d'une barrière d'énergie libre dans le processus de translocation, même lorsqu'une telle barrière n'existe pas. Notre modèle réduit fortement le temps de simulation comparé aux simulations de dynamique moléculaire traditionnelles (quelques secondes contre quelques mois pour un système similaire). Cette accélération provient de l'idéalisation des portions du polymère à l'extérieur du pore. Une telle idéalisation est également présente dans les modèles largement utlisés de type Fokker-Planck, mais dans notre cas le comportement de la partie de la chaîne confinée dans le pore est mieux modélisé.Enfin nous réalisons des expériences pour tester l'existence d'un flot électro-osmotique (EOF) à travers le nanopore d'alpha-hémolysine de staphylococcus aureus. Malgré de nombreux travaux ces dernières années, la question de l'EOF à travers l'un des nanopores biologiques les plus utlisés fait toujours débat. Nous montrons qu'un EOF existe à travers l'alpha-hémolysine et qu'il contrôle la fréquence d'entrée et le temps de résidence de molécules neutres (beta-cyclodextrines) dans le nanopore. La force de l'EOF dépend du type de cation en solution. En particulier nous montrons que l'EOF est plus fort en présence de LiCl que de KCl. / Translocation, the passage of a macromolecule through a pore inserted in a membrane, is involved in many biological processes. Examples include the transport of RNA or proteins between cell components, and the infection of a cell by the passage of a viral DNA through the cell membrane. Today translocation is also the basis of technological applications, such as using pores as sensors for fast molecule sequencing or molecular sieves. The comprehension of the translocation process is important both from a fundamental point of view and for the design of new translocation setups for specific uses.In this thesis both experiments and computer simulations are used to investigate some of the most important effects at work during translocation.Coarse-grained computer simulations are used to study qualitatively the influence of an attractive interaction between the pore walls and a translocating polymer. The location of the interaction is shown to influence both the entry frequency and residence time of the polymer in the pore. The entry frequency is greater when the pore entry is attractive. The behaviour of the residence time with the polymer length is qualitatively and quantitatively affected by the location of the interaction within the pore. Nevertheless, regardless of the location of the interaction, a linear increase of the residence time with polymer length occurs when the polymer becomes longer than the pore. This observation is in qualitative agreement with published experimental data.In the case of slow translocation the correlation between the movements of the monomers confined in the pore may be important. This effect has not been considered previously. A new model of polymer translocation, inspired by the asymmetric exclusion process (ASEP), is developped which enables to specifically investigate this effect. The correlated movements of the monomers confined in the pore are shown to give rise to a behaviour of the residence time with polymer length which is qualitatively similar to what is usually interpreted as the presence of a free-energy barrier in the translocation process, even when such barrier is absent. Our model greatly reduces the simulation time compared to traditional molecular dynamics simulations (several seconds versus several months for similar systems). This speed up comes from the idealization of the portions of the polymer outside the pore. Such idealization is also present in the widely used Fokker-Planck models, but in our case the behaviour of the portion of the chain confined in the pore is better modelled.Finally, experiments are performed to probe the existence of an electro-osmotic flow (EOF) through the nanopore of alpha-hemolysin, from staphylococcus aureus. Despite numerous works during past years, the question of EOF through one of the most commonly used biological nanopores is still under debate. An EOF is shown to exist through alpha-hemolysin and to control the entry frequency and residence time of neutral molecules (beta-cyclodextrins) in the nanopore. The strength of the EOF depends on the type of cations in solution. In particular EOF is shown to be stronger in LiCl solution than in KCl solution.

Un nanopore artificiel est une ouverture de taille nanométrique faite dans un film mince synthétique (polymère ou inorganique). Un nanopore unique peut être considéré comme l’élément simple constitutif d’une membrane. Les récentes avancées dans ce domaine ont ouvert des opportunités pour développer des outils pour la détection de molécules cibles à faible concentration (fmol L-1), en temps réel. Les nanopores artificiels s’inspirent des canaux biologiques situés dans la membrane cellulaire. Ces derniers permettent le transport d’ions ou de molécules entre les milieux intra- et extra-cellulaires, grâce à leurs fortes sélectivités ou leurs propriétés d’ouverture/fermeture. Comparé à leurs homologues biologiques, les limitations des nanopores solides sont leurs manques de sélectivité et de réponse aux stimuli extérieurs. Toutefois, les nanopores solides ont l’avantage d’être beaucoup plus résistant, robuste et facile à manipuler que les pores biologiques. Ainsi la fonctionnalisation de leur surface, avec des systèmes plus ou moins complexes, permettrait d’améliorer à la fois leurs propriétés de transport sélectif, leurs capacités de détection de biomolécules ou encore d’étudier plus précisément les mécanismes fondamentaux du transport des macromolécules en milieu confiné.Dans cette thèse, nous avons conçu dans un premier temps des nanopores bi-fonctionnels, répondant au pH, et à l’attache d’un ligand. Pour fabriquer ces nanopores bi-fonctionnels, nous avons utilisé un système biotine-avidine fixé dans des nanopores polymères. Nous avons démontré qu’il est possible de moduler l’ouverture et la fermeture du nanopore avec le pH de façon réversible. De plus, il est possible de détecter des protéines biotinylées et des anticorps par l’analyse des rectifications de courant. Le principal défaut de cette stratégie est son irréversibilité. En utilisant une stratégie similaire combinée avec des polyélectrolytes, nous avons obtenu des fonctionnalisations réversibles. Ils permettent de moduler la sélectivité ionique du pore et les propriétés de conduction en fonction du pH et de ligand. Dans un second temps, nous nous sommes intéressés aux questions fondamentales de la translocation de polynucléotide, plus précisément de l’analyse de l’influence de l’état de surface du nanopore (hydrophobicité, charge), dans les conditions où la distance de Debye devient équivalente au diamètre du nanopore. Nous avons démontré que si le nanopore présente la même charge que la PolyAdénosine et la PolyCytosine, la vitesse de passage de la molécule augmente et la barrière globale d’énergie d’entrée du nanopore diminue par rapport au nanopore non-chargé hydrophobe. Ensuite, en modifiant la surface d’un nanopore en PET, nous avons montré qu’il est possible de détecter des brins simples et doubles d’ADN très courts (10 à 40 bases). Enfin, nous avons tenté une fonctionnalisation de nanopores pour éviter l’adsorption non spécifique des protéines afin d’étudier la translocation de longs fibrilles d’amyloïdes de lysozyme. Cet objectif n’a pas été complètement atteint compte tenu des résultats qui ne permettent pas d’affirmer quand au passage des molécules à travers le pore.Dans cette thèse nous nous sommes attachés à montrer l’intérêt et la nécessité de fonctionnaliser les pores, aussi bien pour obtenir des nanopores biomimétiques stimuli-répondants (pH et ligand) ou anti-bioadhérants que pour des études fondamentales de transport. Il est également facile de transposer cette technique à des membranes multipores. Il est donc possible de concevoir des membranes optimisées pour des applications de séparation ionique, de capture de molécules cibles ou plus généralement de filtration. / Artificial nanopores are nanometer sized aperture made in synthetic thin films (polymer or inorganic). A single nanopore can be considered as a constitutive element from membranes. Recent advances in this field are bringing new tools for real time detection of target molecules at low concentration (fmol L-1). Biological channels inside the cell membrane are used as models to design solid-state nanopores. They allow ions or molecules transport through intra- and extra-cellular side, thanks to their high selectivity and their gating properties. Compared to their biological counterparts, limitations of the synthetic nanopores are their lack of selectivity and unresponsiveness towards external stimuli. However, the solid state presents several advantages compared to the biological ones, such as nanopores robustness, the control of the number of pores and a long lifetime (several days or weeks). Thus their surface functionalization would increase their selective transport properties, their abilities to detect biomolecules or to study more in details their fundamental mechanisms.In this thesis, we design first bi-functional nanopores, pH- and ligand-gated. To do it, we used biotin-avidin system grafted inside a polymeric nanopore. We demonstrated that it is possible to reversibly gate the nanopore with pH modulation. Moreover, we are able to detect protein labeled with biotin and antibodies by analyzing the current rectification. The major drawback comes from the irreversibility of its covalent bonds. By using a similar concept combined with polyelectrolytes, we obtain a reversible functionalization. Depending on the ligand, the ionic selectivity and the conduction properties can be modulated. Next, we focused on fundamental questions regarding polynucleotides translocation, and more precisely on the influence of the surface state of the nanopore (hydrophobicity, charge) when the Debye distance is similar to the pore diameter. We show that if the nanopore has the same charge as the polyAdenosine or polyCytosine, the translocation time decreases, and the energy barrier of entrance decreases compared to an uncharged hydrophobic nanopore. Then, by modifying the surface of the nanopore made in PET film, we are able to detect short single and double strand of DNA (10 to 40 bases). Finally, we tried to functionalize PET nanopores to avoid unspecific adsorption of proteins and to study the translocation of long fibrils of amyloids from lysozyme. This goal has not been entirely reach since we cannot claim that the fibrils translocate through the pore.In this thesis we show the interest and the need to functionalize the nanopores, to obtain biomimetic stimuli-responsive (pH and ligand), to avoid unspecific adsorption or to study transport properties with the nanopore. It is easy to upscale those techniques to multipores membranes. Thus it is possible to design membranes to enhance their ionic separation, target molecule detection or more generally filtration applications.

In this thesis, underlying concepts of transport phenomena through generated nanopores on a cell membrane during electroporation were studied. A comprehensive literature review was performed to find the pros and cons of the previous works and consequently extensive studies were accomplished to explain shortcomings of the former studies on this topic. The membrane permeabilization of the single cell located in the microchannel was studied, and the effects of microchannel’s wall and electrode size were investigated on cell electroporation. It was studied how the electrical (e.g., strength of the electric pulse) and geometrical parameters (e.g., microchannel height and electrode size) affect size, location, and number of created hydrophilic pores on the cell membrane. Because of a transmembrane potential, the electrokinetic effects have decisive influence on the transport process through the created nanopores. A comprehensive study was performed to explain the electrokinetic transport through the nanochannels. Effects of surface electric charge and radius of the nanochannel on the electric potential, liquid flow, and ionic transport were investigated. Unlike microchannels, the electric potential field, ionic concentration field, and velocity field are strongly size-dependent in the nanochannels. They are also affected by the surface electric charge of the nanochannel. More counter ions than co-ions are transported through the nanochannel. The ionic concentration enrichment at the entrance and the exit of the nanochannel is completely evident from the simulation results. The study also shows that the fluid velocity in the nanochannel is higher when the surface electric charge is stronger, or the radius of the nanochannel is larger. The obtained model of the electrokinetic effects in the nanochannels was utilized to examine the ionic mass transfer and the fluid flow through the generated hydrophilic nanopores of the cell membrane during electroporation. The results showed how the electric potential, velocity field, and ionic concentration vary with the size and angular position of the generated nanopores of the cell membrane. It was also shown that, in the presence of the electric pulse, the electrokinetic effects (the electroosmosis and the electrophoresis) had significant influences on the ionic mass transfer through the nanopores, while the effect of diffusion on the ionic mass flux was negligible in comparison with the electrokinetics. Increasing the radius of the nanopores intensified the effect of convection (electroosmosis) in comparison with the electrophoresis on the ionic flux. Furthermore, the electrokinetic motion of the nanoparticle through the nanochannel was investigated to mimic inserting the nanoscale biological samples, such as QDots and DNAs, through the created nanopores on the cell membrane. It was proved that, because of the large applied electric field over the nanochannel, the impact of the Brownian force was negligible in comparison with the electrophoretic and the hydrodynamic forces. It was demonstrated that increasing the bulk ionic concentration or the surface charge of the nanochannel will increase the electroosmotic flow, and hence affect the particle’s motion. It was also shown that, unlike the microchannels with thin EDL, the change in the nanochannel size will change the EDL field and the ionic concentration field in the nanochannel, affecting the particle’s motion. If the nanochannel size is fixed, a larger particle will move faster than a smaller particle under the same conditions. Finally, it was examined how the nanoscale biological samples (nanoparticles) reach openings of the generated nanopores on the cell membrane during electroporation. It was examined what forces (electrophoresis, diffusion, and convection) brings the nanoparticles into the nanopores and how the size and the surface electric charge of the nanoparticle affect its transport to the opening of the nanopores.

The integration of droplet microfluidics devices with nanopore sensors offers a powerful and miniaturized sensing platform. Such devices can utilize the pre-processing capabilities of microfluidics in conjunction with single molecule sensing offered by nanopores. Microfluidics devices utilizing segmented flow (droplets) allow the compartmentalization of chemical and biological reagents in droplets reducing the processing time and associated cost, which is advantageous to biomolecular applications. Droplet microfluidics have been used in diagnostics and therapeutic applications such as cell and biomarker detection, gene amplification, and drug delivery. Nanopore sensors are currently used in investigating DNA and gene detection, protein-protein interactions, protein folding, and enzymatic kinetic reactions. This thesis proposes a design and outlines a methodology to integrate nanopore sensors within a droplet microfluidic device. The chapters are organized in highlighting three main objectives. The first objective is creating the segmented flow of oil-KCl droplets using a T-junction microfluidic design. The second objective is measuring the conductance of the segmented flow prior to the nanopore integration by using two side channel-AgCl electrodes. Subsequently, the third objective is integrating the droplet microfluidic device with a silicon nitride chip for nanopore fabrication. The nanopore is then created using controlled dielectric breakdown (CBD) method for DNA detection within droplets. The results show the feasibility of sensing individual DNA molecules within droplets using a nanopore sensor. The implemented approach expands upon nanopore applications to detect different samples simultaneously, fast food-borne pathogens and tumor discrimination in cancer biology. We anticipate that this integration is the future of nanopore sensors.

Single molecule nanopore spectroscopy is a label-free method for characterizing a wide variety of water-soluble molecules. Recently there have been efforts to expand nanopore sensing to new areas of study. Forensic investigators require an easy to deploy method to identify an unknown number of contributors in a solution. Currently there is no easily available method to distinguish between a single or multiple contributor solution of DNA before being processed by more advanced analytical techniques which has led to wasted time and resources increasing the backlog of samples waiting to be processed. In this work we present a new nanopore technique capable of distinguishing between single and multiple contributors with an easy to deploy infrared heating laser. Previous cluster-nanopore enhancement interaction studies, produced by this group, have found that polymers in the presence of a gold-nanopore complex spend longer periods of time inside the pore. This is of great interest to the nanopore sensing community because longer residence times enable more accurate statistics on single polymers. In order to understand why x some polymers see large enhancements in the residence times (i.e. 20x) while other polymers see much less enhancement (i.e. 3x) a more complete picture of the free energy components is required. By using a IR heating laser, we construct an Eyring transition graph to extract the enthalpic and entropic energy components to find entropy plays a more important role than previously thought when a polymer interacts with a the nanopore. For nanoconfined polymers, entropy plays an important role on how a polymer will interact with the cluster-nanopore structure which in turn may lead to an increase or decrease of the residence time enhancement factor. This work shows with the addition of an infrared laser heater to a nanopore system a new tool has been added to the field. The IR laser coupled to a nanopore system allows for precise adjustments to residence times of events and extracts the free energy components without the need to physically modify the nanopore.

The specific manner in which ions associate with a peptide surface is a subject of much research. The models currently proposed tend to rely either on computational results from overly simplified systems, or on observations of bulk solution behavior not applicable to peptide solvation. Herein we demonstrate a new platform for directly measuring specific ion interactions with peptides and use a pair of highly conserved model peptides to investigate specific mechanisms by which ions interact with a peptide surface. A system for investigation of charge selective ion-peptide interactions using a conical glass nanopore was designed. The glass nanopore was coated using layer-by-layer depositions of poly(diallyldimethylammonium) chloride and sodium poly(styrenesulfonate) to control the size and charge selectivity of the nanopore. The tip of this nanopore probe was encapsulated in a 5% agarose gel to prevent peptide fouling. This probe was then used to measure the partitioning of cations to or from the surface of two model peptides: nonpolar V5-120 and positively charged KV6-112 elastin-like polypeptide (ELP). Partitioning was measured by clamping the current through the pore at zero amps and measuring the resulting potential across the nanopore. This potential was used to determine the bulk concentration of electrolyte in a 1 mg/mL peptide in 0.1 M electrolyte solution. Measurements were made with a patch clamp using chloride salts with the cations potassium, lithium, cesium, ammonium, and guanidinium at both room temperature and in an ice bath to ensure that the peptides were in their unfolded state and thus that all possible binding sites were exposed to the solution. All salts were observed to partition to the peptide surface with much less affinity than water, resulting in an increase in the bulk electrolyte concentration with the exception of ammonium, which showed a greater affinity than water for the KV6-112 ELP in the ice bath measurements. These results demonstrate that cations do not favorably partition to nonpolar or cationic peptide surfaces.

abstract: Solid-state nanopore research, used in the field of biomolecule detection and separation, has developed rapidly during the last decade. An electric field generated from the nanopore membrane to the aperture surface by a bias voltage can be used to electrostatically control the transport of charges. This results in ionic current rectification that can be used for applications such as biomolecule filtration and DNA sequencing. In this doctoral research, a voltage bias was applied on the device silicon layer of Silicon-on-Insulator (SOI) cylindrical single nanopore to analyze how the perpendicular gate electrical field affected the ionic current through the pore. The nanopore was fabricated using electron beam lithography (EBL) and reactive ion etching (RIE) which are standard CMOS processes and can be integrated into any electronic circuit with massive production. The long cylindrical pore shape provides a larger surface area inside the aperture compared to other nanopores whose surface charge is of vital importance to ion transport. Ionic transport through the nanopore was characterized by measuring the ionic conductance of the nanopore in aqueous hydrochloric acid and potassium chloride solutions under field effect modulation. The nanopores were separately coated with negatively charged thermal silicon oxide and positively charged aluminum oxide using Atomic Layer Deposition. Both layers worked as electrical insulation layers preventing leakage current once the substrate bias was applied. Different surface charges also provided different counterion-coion configurations. The transverse conductance of the nanopore at low electrolyte concentrations (<10-4 M) changed with voltage bias when the Debye length was comparable to the dimensions of the nanopore. Ionic transport through nanopores coated with polyelectrolyte (PE) brushes were also investigated in ionic solutions with various pH values using Electrochemical Impedance spectroscopy (EIS). The pH sensitive poly[2–(dimethylamino) ethyl methacrylate] (PDMAEMA) PE brushes were integrated on the inner walls as well as the surface of the thermal oxidized SOI cylindrical nanopore using surface-initiated atom transfer radical polymerization (SI-ATRP). An equivalent circuit model was developed to extract conductive and resistive values of the nanopore in ionic solutions. The ionic conductance of PE coated nanopore was effectively rectified by varying the pH and gate bias. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2015