Membrane-bound proteins and charged lipids are separated based on their charge-to-size ratio by electrophoretic-electroosmotic focusing (EEF) method on supported lipid bilayers (SLBs). EEF uses opposing electrophoretic and electroosmotic forces to focus and separate proteins and lipids into narrow bands from an initially homogeneous mixture. Membrane-associated species were focused into specific positions within the SLB in a highly repeatable fashion. The steady-state focusing positions of the proteins could be predicted and controlled by tuning experimental conditions, such as buffer pH, ionic strength, electric field and temperature. Careful tuning of the variables should enable one to separate mixtures of membrane proteins with only subtle differences. The EEF technique was found to be an effective way to separate protein mixtures with low initial concentrations and it overcame diffusive peak broadening problem. A "SLB differentiation" post-separation SLB treatment method was also developed by using magnetic particles to rapidly slice the whole SLB into many small patches after electrophoretic separation, while keeping the majority of materials on surface and avoiding the use of chemical reactions. Label-free detection techniques were also developed based on EEF on SLBs. First, a new separation based label-free detection method was developed based on the change of focusing position of fluorescently labeled ligands. This technique is capable of simultaneous detecting multiple protein competitive binding on the same ligand on SLBs. Low concentration protein can be detected in the presence of interfering proteins and high concentration of BSA. The fluorescent ligands were moved to different focusing positions in a charged SLB patch by different binding proteins. Both free ligand and protein bound ligand concentrations were obtained. Therefore, both protein identity and quantity information were obtained simultaneously. Second, the focusing position of fluorescent biomarkers on SLB was used to monitor the phospholipase D catalyzed hydrolysis of phosphatidylcholine (PC) to form phosphatidic acid (PA), which is involved with the change of charge on the phospholipids. The focusing position of fluorescent membrane-bound biomarker in the EEF experiment is directly determined by the negative charge density on SLB. Other enzyme reactions involved with the change of phospholipids charge can be monitored in a label-free fashion in a similar way.

No description available.

Die markierungsfreie Detektion von molekularen Wechselwirkungen mittels Feldeffekt-basierter Sensoren ist eine vielversprechende Strategie zur Entwicklung einer neuen Generati-on von Biochips mit direkter elektrischer Auslesung und somit geeignet für schnelle, einfache und kostengünstige Analysen. In dieser Arbeit wurde als Transducer eine kapazitive Elektrolyt-Isolator-Silizium- (EIS) Struktur zur markierungsfreien elektrischen Detektion geladener Makromoleküle anhand ihrer intrinsischen Ladung verwendet. Als Modellsystem für die Untersuchung der im EIS-Sensor durch die Ausbildung „planarer“ bzw. „brush“-ähnlicher Molekülschichten induzierten Effekte wurden Polyelektrolyt-Multischichten (PEM) bzw. DNA-Moleküle verwendet. Die Adsorption der positiv und negativ geladenen Polyelektrolyt-Schichten an die Sensor-Oberfläche, sowie der Einfluss der Polyelektrolyt-Konzentration, der Ionenstärke und der Art des Elektrolyten auf das EIS-Signal wurden elektrochemisch untersucht. Zusätzlich wurde die Ausbildung der PEM physikalisch unter Verwendung eines Rasterkraftmikroskopes und der Ellipsometrie charakterisiert. Basierend auf Silizium-Isolator-Silizium-Strukturen wurde zum ersten Mal ein Mikroarray mit „Nanoplate“ EIS-Sensoren entwickelt, die alle auf einem einzigen Chip integriert waren. Dies ermöglicht mittels differenzieller Messanordnungen eine verlässliche Detektion der DNA-Hybridisierung bzw. -Denaturierung. Die Eigenschaften des Biosensors wurden durch Verwendung von Gold-Nanopartikeln für die Immobilisierung der DNA auf der Sensorober-fläche sowie durch eine niedrige Salzkonzentration im Messpuffer entscheidend verbessert. Die Ergebnisse dieser neuen Vorgehensweise wurden mittels Fluoreszenz-Mikroskopie vali-diert. Darüber hinaus wurde ein elektrostatisches Modell für einen EIS-Sensor mit einer „planaren“ und einen weiteren, mit „brush“-ähnlicher Molekularschicht entwickelt. Das Modell prognos-tiziert eine starke Abhängigkeit der Sensorsignalstärke von der Elektrolytkonzentration, der Ladungsdichte auf der Oberfläche und dem Abstand zwischen geladener Schicht und Sensor-oberfläche. Die Prognosen stimmten durchweg gut mit den experimentellen Ergebnissen überein. / Label-free detection of molecular interactions utilizing field-effect devices is one of the most attractive approaches for a new generation of biochips with direct electrical readout for a fast, simple and cost-effective analysis. In this study, a capacitive electrolyte-insulator-semiconductor (EIS) structure was used as transducer for the label-free electrical detection of charged macromolecules via their intrinsic charge. Polyelectrolyte multilayers (PEM) and DNA molecules were utilized as model systems to study the charge effects induced in EIS sensors by the formation of “planar”- and “brush”-like molecular layers, respectively. The layer-by-layer adsorption of positively and negatively charged polyelectrolyte (PE) layers onto the sensor surface as well as the influence of PE concentration, ionic strength and type of the applied electrolyte on the EIS sensor signal was electrochemically studied. In addition, the PEMs build-up was physically characterized using atomic force microscopy, scanning electron microscopy and ellipsometry. An array of on-chip integrated nanoplate EIS sensors based on a silicon-on-insulator structure was developed for the first time, enabling the reliable detection of DNA hybridiza-tion/denaturation in a differential measurement setup. Enhanced DNA biosensor characteris-tics were achieved by the immobilization of DNA molecules on the sensor surface via Au-nanoparticles and used low-concentrated buffer solution for the measurements. The results of this novel approach were validated by means of the fluorescence microscopy method. Furthermore, an electrostatic model for an EIS sensor modified with “planar”- and “brush”-like molecular layers was developed. The model predicts a strong dependence of the sensor signal on the electrolyte concentration, surface charge density and the distance between the charged layer and the sensor surface. This is consistently agreeing with the experimental re-sults.

Le marché du diagnostic connait un essor considérable depuis l’avènement de labiologie moléculaire. Plus précis et souvent plus rapide, le diagnostic moléculaire in vitro(DIV) est de plus en plus utilisé dans les laboratoires d’analyses médicales. L’ensemble destests dédiés au marché du DIV répond à des contraintes socio-économiques très précisescomme : la fiabilité du résultat, le délai de réponse court, le faible coût et la facilitéd’utilisation. Les indicateurs socio-économiques montrent que la technologie des biopuces estun potentiel bon candidat pour répondre aux attentes du marché. En effet, cet outil permetl’analyse simultanée de plusieurs dizaines voire centaines de séquences nucléiques et doncl’identification d’autant d’organismes en une seule analyse. Cette technologie s’inscrit encomplément de la PCR en apportant l’avantage de l’analyse multiplexée à moyen débit. Deplus, elle permet de donner une réponse globale de la multiplicité des espèces présentes dansl’échantillon sans avoir besoin de passer par une étape de culture. Néanmoins, cettetechnologie n’est pas optimisée pour le marché du DIV. En effet, son usage est complexe, peurobuste et trop cher pour concurrencer les méthodes actuelles (microbiologie pasteurienne,PCR, Elisa, etc..). Dans le but de réduire le coût de fabrication des biopuces à ADN, il estdonc nécessaire de développer des méthodes alternatives. Dans un premier temps, l’objectif de cette thèse Cifre a été de mettre au point unprototype nouveau de dépôt de biomolécules basé sur la lithographie douce, permettant dedéposer les oligonucléotides sondes de façon multiplexée et selon des motifs micrométriques.Cette nouvelle technologie a été évaluée par rapport aux technologies de références. Puis,nous avons développé un procédé innovant de double fonctionnalisation de surface. Ceprocédé simple et rapide a pour avantages de fonctionnaliser la biopuce avec la chimie desurface et les sondes en une seule étape et d’augmenter les signaux d’hybridation. La secondepartie de la thèse a été de coupler cette nouvelle technologie à la détection des événementsd’hybridation sans marquage en utilisant la diffraction de la lumière. La principale différenceavec la méthode de détection par fluorescence repose sur l’adressage des sondes. En effet, ledépôt doit être réalisé sous forme de réseaux de lignes nanométriques diffractants de façon àce que l'interaction entre les molécules déposées et les cibles qui interagissent soit trèssensible. Cette seconde phase du projet a été très ambitieuse et innovante. La faisabilité decette méthode de détection, démontrée par des simulations théoriques, a fait l’objet d’untravail d’optimisation très important et les résultats obtenus montrent que cette technologiesans marquage est possible. / The diagnosis market increased since the advent of molecular biology. More precise and often faster, the in vitro molecular diagnosis (DIV) is more and more used in medical analyses laboratories. DNA chips technology seems to be a good candidate to answer the market expectations. Indeed, this tool allows making several hundreds of analyses simultaneously. Furthermore, it allows giving a global answer of all the present species in the sample without the need of a culture step. Nevertheless, this technology is not optimized for the market of the DIV. Indeed, its use is complex and too expensive in comparison with the current methods (Pasteur microbiology, PCR, Elisa, etc.). So it is necessary to develop an alternative method to reduce the manufacturing cost and simplify the use of DNA chips. First, the goal of this industrial PhD Cifre supported by the Dendris Company was to complete a new prototype of biomolecules deposition based on soft lithography, allowing multiplexing the deposition of oligonucleotides probes along micro and nanometric patterns.This new technology was compared with the reference technologies. Then, we developed an innovative process of surface co-functionalization. This simple and fast process permits to functionalize the DNA chips with both surface chemistry and probes in a single step and to increase the hybridization signals. The second part of this PhD thesis was to couple this new technology with label-free detection using light diffraction. The main difference with fluorescence-based detection was about probes patterning. Indeed, we needed to generate molecular gratings of nanometric lines to diffract efficiently light from a laser beam. We showed that the absolute diffraction intensity increase with the gratings thickness, which is directly correlated with, probes and targets interactions. The second phase of the project was very ambitious and innovative because we demonstrated the feasibility of this label-free detection. And now we can think that this technology will appear as an alternative method for the diagnosis

Des substrats SERS, élaborés selon une approche simple et à moindre coût, ont été étudiéspour la détection sans marqueurs d’ADN en vue d’applications dans le domaine du diagnostic médical.Un protocole de réduction photocatalytique assistée chimiquement conduisant à des hétérostructuresAg°/TiO2 a été optimisé. Nohttp://star.theses.fr/editeur.jsp?tefId=58411&action=save#droitsus avons montré en quoi l’utilisation d’un agent encapsulant et d’uneprocédure de nucléation-croissance permettent de contrôler la formation et l’agrégation de NPs Ag° à lasurface de couches minces TiO2. L’agrégation contrôlée des NPs conduit à des points chauds induisantune très forte amplification de l’effet SERS. Les performances des substrats SERS ont tout d’abord étévalidées par détection Raman de la molécule modèle R6G. Des études de fond, portant sur la détectionde polybases dérivées des quatre nucléobases constituant la structure de l’ADN, adénine, cytosine,guanine et thymine, ont ensuite été réalisées. Le potentiel de détection des hétérostructures Ag°/TiO2 apermis l’indexation quasi-intégrale des bandes Raman des quatre polybases étudiées, modifiées ou nonavec des groupements NH2, et nous a permis de discuter des effets d’accrochage, d’orientation etd’agencement des molécules d’ADN sur les substrats SERS. Des études complémentaires ont finalementconfirmé le potentiel de nos hétérostructures en fournissant différents aperçus sur l’hybridation despolybases et l’association de différentes polybases sur un même substrat SERS. / SERS substrates, elaborated through a simple and low-cost procedure, have been studied forthe label-free detection of DNA in the view of applications in the medical diagnostic field. A chemicallyassisted photocatalytic reduction protocol leading to an Ag°/TiO2 heterostructure has been optimized.We have shown how the use of an encapsulating agent and a nucleation-growth procedure enable tocontrol the formation and aggregation of Ag° NPs at the surface of TiO2 thin films. The controlledaggregation of NPs leads to hot points inducing a very strong amplification of the SERS effect.Performances of the SERS substrate have first been evaluated through the Raman detection of the R6Gmodel molecule. Thorough studies dealing with the detection of polybases derived from the fournucleobases constituting the DNA structure, adenine, cytosine, guanine, and thymine, have then beenconducted. The detection potential of the Ag°/TiO2 heterostructure enabled a nearly exhaustiveindexation of the Raman bands for the four studied polybases, modified or not with NH2 groups, and todiscuss on binding, orientation, and ordering effects of the DNA molecules on the SERS substrate.Complementary studies finally enabled us to confirm the potential of our heterostructure by providingdifferent insights on the polybase hybridization and the association of different polybases on a sameSERS substrate.

The electromagnetic absorption properties of plasmonic nanostructures were utilized to develop mesoscopic sites for highly efficient photothermal generation steam, SERS biosensing, and light-triggered cellular delivery uptake. Plasmonic nanostructures embedded in common thermal solutions produces vapor without the requirement of heating the fluid volume. When particles are dispersed in water at ambient temperature, energy is directed primarily to vaporization of water into steam, with a much smaller fraction resulting in heating of the fluid. Solar illuminated aqueous nanoparticle solution can drive water-ethanol distillation, yielding fractions significantly richer in ethanol content than simple thermal distillation and also produced saturated steam destroying Geobacillus stearothermophilus bacteria in a compact solar powered autoclave. Subwavelength biosensing sites were developed using the plasmonic properties of gold nanoshells to investigate the properties of aptamer (DNA) target complexes. Nanoshells are tunable core-shell nanoparticles whose resonant absorption and scattering properties are dependent on core/shell thickness ratio. Nanoshells were used to develop a label free detection method using SERS to monitor conformational change induced by aptamer target binding. The conformational changes to the aptamers induced by target binding were probed by monitoring the aptamer SERS spectra reproducibility. Furthermore, nanoshells can serve as a nonviral light-controlled delivery vector for the precise temporal and spatial control of molecular delivery in vitro. The drug delivery concept using plasmonic vectors was shown using a monolayer of ds-DNA attached to the nanoshell surface and the small molecular “parcel” intercalated inside ds-DNA loops. DAPI, a fluorescent dye, was used as the molecular parcel to visualize the release process in living cells. Upon laser illumination at the absorption resonance the nanoshell converts photon energy into heat producing a local temperature gradient that induces DNA dehybridization, releasing the intercalated molecules.

L‐glutamate is associated with several neurological disorders; thus, monitoring fast dynamics of L‐glutamate is of great importance in the field of neuroscience. Electrode miniaturization demanded by many applications leads to reduced surface area and decreased amounts of immobilized enzymes on coated electrodes. As a result, lower signal‐to‐noise ratios are observed for oxidase‐enzyme based sensors. To increase the signal‐to‐noise ratio we have developed a process to fabricate micro‐ and nano‐ structures on the microelectrode surface. Localized surface‐plasmon resonances (SPR) has been extensively used to design label‐free biosensors that can monitor receptor‐ligand interactions. A major challenge with localized SPR sensors is that they remain highly susceptible to interference because they respond to both solution refractive index changes and surface binding of the target analyte. The key concept introduced in the present work is the exploitation of transverse and longitudinal resonance modes of nanorod arrays to differentiate between bulk refractive index changes and surface interactions. The transverse bulk sensitivity of the localized SPR sensor (107 nm/RIU) remains competitive with typical single mode gold nanosphere SPR sensors. The figure of merit for the device’s cross‐sensitivity (1.99) is comparable to that of typical wavelength‐interrogated propagating SPR sensors with self referencing.

Des substrats SERS, élaborés selon une approche simple et à moindre coût, ont été étudiéspour la détection sans marqueurs d’ADN en vue d’applications dans le domaine du diagnostic médical.Un protocole de réduction photocatalytique assistée chimiquement conduisant à des hétérostructuresAg°/TiO2 a été optimisé. Nohttp://star.theses.fr/editeur.jsp?tefId=58411&action=save#droitsus avons montré en quoi l’utilisation d’un agent encapsulant et d’uneprocédure de nucléation-croissance permettent de contrôler la formation et l’agrégation de NPs Ag° à lasurface de couches minces TiO2. L’agrégation contrôlée des NPs conduit à des points chauds induisantune très forte amplification de l’effet SERS. Les performances des substrats SERS ont tout d’abord étévalidées par détection Raman de la molécule modèle R6G. Des études de fond, portant sur la détectionde polybases dérivées des quatre nucléobases constituant la structure de l’ADN, adénine, cytosine,guanine et thymine, ont ensuite été réalisées. Le potentiel de détection des hétérostructures Ag°/TiO2 apermis l’indexation quasi-intégrale des bandes Raman des quatre polybases étudiées, modifiées ou nonavec des groupements NH2, et nous a permis de discuter des effets d’accrochage, d’orientation etd’agencement des molécules d’ADN sur les substrats SERS. Des études complémentaires ont finalementconfirmé le potentiel de nos hétérostructures en fournissant différents aperçus sur l’hybridation despolybases et l’association de différentes polybases sur un même substrat SERS. / SERS substrates, elaborated through a simple and low-cost procedure, have been studied forthe label-free detection of DNA in the view of applications in the medical diagnostic field. A chemicallyassisted photocatalytic reduction protocol leading to an Ag°/TiO2 heterostructure has been optimized.We have shown how the use of an encapsulating agent and a nucleation-growth procedure enable tocontrol the formation and aggregation of Ag° NPs at the surface of TiO2 thin films. The controlledaggregation of NPs leads to hot points inducing a very strong amplification of the SERS effect.Performances of the SERS substrate have first been evaluated through the Raman detection of the R6Gmodel molecule. Thorough studies dealing with the detection of polybases derived from the fournucleobases constituting the DNA structure, adenine, cytosine, guanine, and thymine, have then beenconducted. The detection potential of the Ag°/TiO2 heterostructure enabled a nearly exhaustiveindexation of the Raman bands for the four studied polybases, modified or not with NH2 groups, and todiscuss on binding, orientation, and ordering effects of the DNA molecules on the SERS substrate.Complementary studies finally enabled us to confirm the potential of our heterostructure by providingdifferent insights on the polybase hybridization and the association of different polybases on a sameSERS substrate.

abstract: Detection of molecular interactions is critical for understanding many biological processes, for detecting disease biomarkers, and for screening drug candidates. Fluorescence-based approach can be problematic, especially when applied to the detection of small molecules. Various label-free techniques, such as surface plasmon resonance technique are sensitive to mass, making it extremely challenging to detect small molecules. In this thesis, novel detection methods for molecular interactions are described. First, a simple detection paradigm based on reflectance interferometry is developed. This method is simple, low cost and can be easily applied for protein array detection. Second, a label-free charge sensitive optical detection (CSOD) technique is developed for detecting of both large and small molecules. The technique is based on that most molecules relevant to biomedical research and applications are charged or partially charged. An optical fiber is dipped into the well of a microplate. It detects the surface charge of the fiber, which does not decrease with the size (mass) of the molecule, making it particularly attractive for studying small molecules. Third, a method for mechanically amplification detection of molecular interactions (MADMI) is developed. It provides quantitative analysis of small molecules interaction with membrane proteins in intact cells. The interactions are monitored by detecting a mechanical deformation in the membrane induced by the molecular interactions. With this novel method small molecules and membrane proteins interaction in the intact cells can be detected. This new paradigm provides mechanical amplification of small interaction signals, allowing us to measure the binding kinetics of both large and small molecules with membrane proteins, and to analyze heterogeneous nature of the binding kinetics between different cells, and different regions of a single cell. Last, by tracking the cell membrane edge deformation, binding caused downstream event – granule secretory has been measured. This method focuses on the plasma membrane change when granules fuse with the cell. The fusion of granules increases the plasma membrane area and thus the cell edge expands. The expansion is localized at the vesicle release location. Granule size was calculated based on measured edge expansion. The membrane deformation due to the granule release is real-time monitored by this method. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2015

Ce travail présente une méthode originale de détection et de quantification, sans étape de marquage, de la proportion de bases libres contenues dans des acides nucléiques. La spectrométrie de diffusion Raman exaltée de surface (DRES ou SERS en anglais) nous a permis d’obtenir la signature spectrale spécifique des nucléotides caractéristiques des ARN (adénosine, cytosine, guanosine et uridine), en utilisant des colloïdes d’argent comme substrat-DRES et des ajouts de MgCl2 comme agent d’agrégation. Les conditions de détection ont été optimisées pour établir un protocole de quantification de la proportion des nucléobases non-appariées par spectrométrie DRES. Les limites de détection obtenues sont de l’ordre de quelques dizaines de picomoles. L’amélioration de la reproductibilité des mesures par spectrométrie DRES passe par le contrôle précis des temps de réaction (adsorption et agrégation), qui peut être contrôlé grâce à l’utilisation de plateformes microfluidiques adaptées. Nous avons mis en œuvre deux types de plateformes microfluidiques, l’une basée sur des écoulements monophasiques et l’autre sur la génération de gouttes. Les espèces à analyser sont contenus dans les gouttes, permettant la détection in situ par spectrométrie DRES des divers nucléotides. / This work deals with the development of an original label-free method for free bases proportions detection and quantification of nucleic acids. The surface enhanced Raman spectroscopy (SERS) allowed obtaining the specific spectral signature of characteristic nucleotides of RNA (adenosine, cytosine, guanosine and uridine), using silver colloids as SERS substrate and MgCl2 addition as aggregating agent. Then, the condition detection have optimizing to establish a label-free quantification protocol of free nucleobases proportion by SERS spectroscopy. The detection limits obtained are order of few picomoles. The reproducibility improvement of SERS detection requires the precise control of time reaction (adsorption and aggregation), which could be control thanks to microfluidic chips use. We have implemented two different microfluidic chips, one based on single-phase flows and one other based on droplets generation. The analyzed species are containing in droplets, allowing in situ detection by spectroscopy SERS of various nucleotides.