The RNA polymerase T7 is utilized as a component of motor complexes in DNA nanotechnology due to its high promotor specificity, the lack of external transcription factors and its very high processivity, but there is no experience of its application on small double stranded DNA circles. Circular templates from 210 to 126 bp in circumference sharing a common promotor termination motif were synthesized and transcription was monitored at end point on gel and in real time with a 2’ O methyl RNA molecular beacon. The RNAP T7 was found to be able to utilize circular dsDNA templates down to 126 bp with moderate impact on transcription rate for saturated systems and rolling circle transcription products were evident with denaturizing PAGE gel electrophoresis for templates down to 167 bp.

[ES] El interés en desarrollar biosensores de alta sensibilidad para identificar y cuantificar una amplia gama de moléculas ha aumentado notablemente durante las últimas décadas en numerosos campos de aplicación. Entre ellos probablemente el más demandado sea el diagnóstico médico, el cual ha sido impulsado por el descubrimiento de nuevos biomarcadores de enfermedades, tales como los miRNAs. No obstante, la mayoría de las técnicas existentes para realizar la detección requieren el uso de marcadores debido a la falta de sensibilidad para detectar analitos en bajas concentraciones. Las estructuras ópticas basadas en campo evanescente, donde la luz es usada para transformar interacciones bioquímicas en variaciones de las señales ópticas, constituyen una interesante alternativa para el desarrollo de este tipo de biosensores sin la necesidad de utilizar marcadores (label-free). Concretamente las estructuras fotónicas integradas en tecnología Silicon On Insulator exhiben alta sensibilidad, bajo límite de detección y alto nivel de multiplexación en aplicaciones de detección, especialmente cuando se utilizan materiales y procesos basados en silicio y compatibles con CMOS. En esta Tesis Doctoral se muestra el desarrollo de un biosensor fotónico integrado label-free para la detección de oligonucleótidos, y más concretamente biomarcadores de cáncer miRNAs. Este biosensor está basado en la combinación de estructuras de band gap fotónico y la inmovilización de sondas de tipo molecular beacon sobre su superficie. La combinación de sendos elementos de transducción y bioreconomiento ha proporcionado una elevada sensibilidad en la detección de oligonucleótidos manteniendo un footprint por debajo de 100 µm2. El uso de este biosensor fotónico ha permitido también estudiar experimentalmente una novedosa técnica de amplificación de detección. Esta técnica explota el cambio conformacional sufrido por la sonda molecular beacon tras la hibridación con su oligonucleótido complementario, permitiendo alejar una partícula/molécula de la superficie del sensor, lo cual podría ser utilizado para amplificar la respuesta de detección del sensor. Finalmente se propone una estrategia de regeneración en línea de los biosensores nanofotónicos desarrollados mediante una estrategia química basada en el uso de formamida. Esta estrategia no solo permite ahorrar tiempo sino que también reduce la variación entre las medidas obtenidas en experimentos diferentes, siendo especialmente útil cuando se testean niveles similares de analito. / [CA] L'interés en desenvolupar biosensors d'alta sensibilitat per a identificar i quantificar una àmplia gamma de molècules ha augmentat notablement durant les últimes dècades en nombrosos camps d'aplicació. Entre ells probablement el més demandat siga el diagnòstic mèdic, el qual ha sigut impulsat pel descobriment de nous biomarcadors de malalties, com ara els miRNAs. No obstant això, la majoria de les tècniques existents per a realitzar la detecció requereixen l'ús de marcadors a causa de la falta de sensibilitat per a detectar anàlits en baixes concentracions. Les estructures òptiques basades en camp evanescent, on la llum és usada per a transformar interaccions bioquímiques en variacions dels senyals òptics, constitueixen una interessant alternativa per al desenvolupament d'aquesta tipus de biosensors sense la necessitat d'utilitzar marcadors (label-free). Concretament les estructures fotòniques integrades en tecnologia Silicon On Insulator exhibeixen alta sensibilitat, baix límit de detecció i alt nivell de multiplexació en aplicacions de detecció, especialment quan s'utilitzen materials i processos basats en silici i compatibles amb CMOS. En aquesta Tesi Doctoral es mostra el desenvolupament d'un biosensor fotònic integrat label-free per a la detecció d'oligonucleòtids, i més concretament biomarcadors de càncer miRNAs. Aquest biosensor està basat en la combinació d'estructures de band gap fotònic i la immobilització de sondes de tipus molecular beacon sobre la seua superfície. La combinació d'ambdós elements de transducció i bioreconeixement ha proporcionat una elevada sensibilitat en la detecció d'oligonucleòtids mantenint un footprint per davall de 100 µm². L'ús d'aquest biosensor fotònic ha permés també estudiar experimentalment una nova tècnica d'amplificació de detecció. Aquesta tècnica explota el canvi conformacional patit per la sonda molecular beacon després de la hibridació amb el seu oligonucleòtid complementari, permetent allunyar una partícula/molècula de la superfície del sensor, la qual cosa podria ser utilitzada per amplificar la resposta de detecció del sensor. Finalment es proposa una estratègia de regeneració en línia dels biosensors nanofotònics desenvolupats mitjançant una estratègia química basada en l'ús de formamida. Aquesta estratègia no sols permet estalviar temps sinó que també redueix la variació entre les mesures obtingudes en experiments diferents, sent especialment útil quan es testen nivells similars d'anàlit. / [EN] The interest in developing highly sensitive biosensors to identify and quantify a wide range of molecules has remarkably been increasing during the last decades in numerous application fields. Among them, medical diagnosis is probably the most demanded, which has been driven by the discovery of new biomarkers of diseases, such as miRNAs. However, most of the existing techniques to perform the detection require the use of labels due to the lack of sensitivity to detect analytes at low concentrations. Evanescent-wave optical structures, where light is used to transduce biochemical interactions into variations of the optical signals, are an interesting alternative for the development of this type of biosensors allowing a label-free detection. Specifically, the planar integrated photonic structures based on Silicon On Insulator technology exhibit an extremely high sensitivity, a low detection limit and a high level of multiplexing in detection applications, especially when using materials and processes based on silicon and being CMOS compatible. This PhD Thesis is focused on the development of label-free integrated photonic biosensors for the detection of oligonucleotides, and more specifically miRNA cancer biomarkers. This biosensor is based on the combination of photonic band gap structures and the immobilization of molecular beacon probes on its surface. The combination of both transduction and biorecognition elements has provided a very high sensitivity towards the detection of target oligonucleotides while keeping a sensor footprint below 100 µm2. The use of this photonic biosensor also allowed the experimental study of a novel detection amplification technique. This technique exploits the conformational change suffered by the molecular beacon probe after hybridization with its complementary oligonucleotide, allowing the displacement of a particle/molecule away from the sensor surface, what might be used for amplifying the sensor's detection response. Finally, an online regeneration strategy for nanophotonic biosensors developed through a chemical strategy based on the use of formamide is proposed. This strategy not only saves time but also reduces the variation between measurements obtained in different experiments, being especially useful when testing similar levels of analyte. / Ruiz Tórtola, Á. (2021). Desarrollo de biosensores nanofotónicos de alta sensibilidad para la detección de biomarcadores microRNA en aplicaciones de diagnóstico médico [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172631 / TESIS

La thérapie photodynamique (PDT) est une technique utilisée cliniquement pour traiter certaines maladies de la peau, la dégénérescence maculaire liée à l’âge et certains types de cancer. Elle fait intervenir trois composants : une molécule photosensible ou photosensibilisateur (PS), la lumière et l’oxygène. Après administration du PS, celui-ci va se localiser plus ou moins sélectivement dans les zones tumorales où il est alors activé par irradiation lumineuse à une longueur d’onde et une puissance données. Ceci engendre la formation d’espèces réactives de l’oxygène (ROS) très réactives, dont l'oxygène singulet1 O2, qui entraînent la destruction des tissus tumoraux par nécrose ou apoptose. Afin d’améliorer la sélectivité du traitement, différentes pistes sont actuellement exploitées dont l’élaboration de « photodynamic molecular beacons » (PMB). Dans un PMB, le photosensibilisateur (PS) est associé via un peptide à un inhibiteur 1O2, appelé quencher. Ce quencher inhibe la formation d’1O2 tant que le composé n’a pas atteint sa cible. Une fois la zone cancéreuse atteinte, des enzymes spécifiques clivent le peptide, libérant ainsi le PS qui retrouve alors sa capacité à former de l’1O2. Trouver un couple PS/quencher adéquat reste un challenge en PDT. Les propriétés photophysiques particulières des caroténoïdes et leur aptitude à inhiber la production d’1O2 font de ces derniers des quenchers potentiellement utilisables pour l’élaboration de PMBs. Chez les plantes, les caroténoïdes (carotènes et xanthophylles) sont des pigments associés à la photosynthèse, qui ont deux rôles principaux : un rôle de collecteur de lumière et un rôle photoprotecteur en protégeant le(s) système(s) photosynthétique(s) contre les dommages photooxydatifs liés à une exposition trop intense à la lumière. Ceci s’opère, entre autre, via le cycle des xanthophylles. Cette aptitude à capter de l’énergie présente un intérêt potentiel à ne pas négliger dans la perspective de la conception de PMB utilisables en thérapie photodynamique. Dans le cadre de cette thèse en co-tutelle avec la Faculté des Sciences de Bizerte nous avons ciblé les caroténoïdes présents dans trois fruits produits en Tunisie à savoir les kakis (Diospyros kaki L.), les abricots (Prunus armeniaca L.) et les pêches (Prunus persica L.) connus pour leur richesse globale en ces pigments. Divers procédés d’extractions ont été étudiés : (i) L’extraction de type Soxhlet par solvants organiques à pression atmosphérique, utilisée comme référence, (ii) l'extraction accélérée par solvant organique (ASE : Accelerated solvent Extraction) effectuée sous pression, enfin (iii) l'extraction par CO2 supercritique avec l’éthanol comme cosolvant. Pour ces deux derniers procédés, une approche par plan d’expériences (surfaces de réponses) a été utilisée pour identifier les facteurs clé et les conditions optimales d’extractions de divers caroténoïdes (pression, température, débit, % de cosolvant, temps, nombre de cycles). L'analyse par chromatographie liquide à haute performance couplée à la détection UV-Visible et à la spectrométrie de masse a ensuite permis l'identification et la quantification des caroténoïdes présents dans les extraits obtenus, permettant ainsi de comparer les profils caroténoïdiques propres à chaque fruit et les performances de chaque procédé d’extraction. Cette étude ayant révélé un profil caroténoïdique particulièrement intéressant chez le kaki par rapport aux autres fruits, une extraction et une purification des caroténoïdes de ce fruit par chromatographie liquide haute pression préparative a ensuite été effectuée afin de disposer d’une quantité suffisante de chaque caroténoïde, et parfois de leurs isomères conformationnels, en vue de l’étude de leurs propriétés photophysiques (absorption, émission de fluorescence, inhibition d’1O2) et de l’évaluation de leur intérêt potentiel en tant que quencher d’1O2 dans un édifice de type PMB / Photodynamic therapy (PDT) is a clinically used technique for treating skin diseases, age-relatedmacular degeneration but mainly some types of cancer. PDT involves three components: a photosensitive molecule named photosensitizer (PS), light and oxygen. After administration of the PS, this one will be located more or less selectively in tumoral regions where it is activated by light irradiation at appropriate wavelength and power. This leads to the formation of highly reactive and cytotoxic reactive oxygen species (ROS), especially singlet oxygen, resulting in the destruction of the tumor by necrosis or apoptosis. To improve the treatment selectivity, different strategies are being exploited, one of which is the development of "photodynamic molecular beacons" (PMB). In PMB the photosensitizer is linked via a peptide to an inhibitor of 1O2 (quencher). This quencher inhibits the formation of 1O2 as long as the compound has not reached its target, namely cancer cells. In order to inhibit the toxicity of the PS in non-target cells and restore toxicity only close to the biological target, it is necessary to find an adequate PS/quencher couple. This remains a challenge for PDT. Carotenoids are interesting candidates due to their specific photophysical properties and ability to inhibit 1O2, which makes them potential quenchers for building PMBs. In plants, carotenoids (carotenes and xanthophylls) are pigments involved in the photosynthesis, in which they play two main roles: a light collecting role and a protecting role by preserving the photosynthetic systems against photoxydative damages induced by a too intense light exposure. This protection can for instance occur via the well-known xanthophylls cycle. This capacity to catch energy presents a potential interest that should not be neglected in the framework of the design of PMBs usable in photodynamic therapy. Within the framework as part of this PhD thesis in Cotutelle with the Faculty of Sciences of Bizerte, we focused on carotenoids from three fruits produced in Tunisia: persimmon (Diospyros kaki L.), apricot (Prunus armeniaca L.) and peache (Prunus persica L.), known for their global richness in these natural pigments. Three extraction processes were investigated: (i) the Soxhlet extraction based on the use of organic solvent at atmospheric pressure and used as reference, (ii) the accelerated solvent extraction (ASE) using organic solvent under high pressure, and (iii) the supercritical fluid extraction (SFE) using supercritical CO2 and ethanol as cosolvent. For these two last processes, a design of experiments (Surface Response Design) was used to identify the key factors and optimal extraction conditions of various carotenoids (pressure, temperature, flow, % cosolvent, time, number of cycles). Then, HPLC-PDA coupled with mass spectrometry (MS) enabled the identification and quantification of carotenoids from the extracts. Thus it was possible to compare the profiles in carotenoids content from each fruit as well as the performances of each extraction process. This study showed that the carotenoidic profile in the persimmon was the most interesting as compared to the profiles in the two other fruits. Extraction and purification of the carotenoids from persimmon by preparative high pressure liquid chromatography were then performed in order to have a sufficient amount of each carotenoid and sometimes of their conformational isomers. We finally performed a study of their photophysical properties (absorption, fluorescence emission, 1O2 inhibition) in order to evaluate their potential as 1O2 quencher in molecular construction such as a PMB

Exogenously supplied organoselenium compounds, capable of propagating a selenium redox cycle, were shown to supplement natural cellular defenses against oxidants generated during biological activity. Phenylaminoalkyl selenides were developed in our laboratory as novel substrate analogs for the enzyme dopamine beta-monooxygenase. Recently, phenylaminoalkyl selenides were found to protect plasmid DNA and Molecular beacons from oxoperoxynitrate – mediated damage by scavenging this oxidant and forming the corresponding selenoxides as the sole selenium – containing products. Rate constants were determined for the reactions of the phenylaminoalkyl selenoxides with GSH at physiological pH and 25 degrees C. The kinetic data obtained in current and previous research was subsequently used in a MatLab simulation, which showed the feasibility of selenium redox cycling by GSH in the presence of a cellular oxidant, oxoperoxynitrate. Loblolly pine (LP, Pinus taeda) is the primary commercial species in southern forests covering 11.7 million hectares. Somatic embryogenesis (SE) is an effective technique to implement production of high value genotypes of LP. SE is a multi-step process, which includes initiation of somatic embryo (SME) growth from tree tissue, maintenance and multiplication of early stage SMEs and the maturation / germination phase. In this work, we isolated a substance from stage 2 or 3 LP female gametophyte (FG) tissue that stimulates early stage SME growth, and characterized this substance as citric acid on the basis of 1H NMR and mass spectrometry. We then demonstrated that topical application of citric acid to SMEs stimulates embryo colony growth at p = 0.05 for 3 of the 5 genotypes tested. Phenylketonuria (PKU) is an autosomal recessive disorder caused by an impaired conversion of L-phenylalanine (L-Phe) to L-tyrosine (L-Tyr). A novel assay based on enzymatic - colorimetric methodology (ECA) was developed in order to detect elevated concentrations of L-Phe in undeproteinized plasma of PKU patients via continuous spectrophotometric detection. We report here that L-Phe concentrations in undeproteinized plasma measured using our ECA were comparable to those determined on an amino acid analyzer based on Pearson correlation coefficients and a Bland and Altman comparison.