abstract: Microfluidic systems have gained popularity in the last two decades for their potential applications in manipulating micro- and nano- particulates of interest. Several different microfluidics devices have been built capable of rapidly probing, sorting, and trapping analytes of interest. Microfluidics can be combined with separation science to address challenges of obtaining a concentrated and pure distinct analyte from mixtures of increasingly similar entities. Many of these techniques have been developed to assess biological analytes of interest; one of which is dielectrophoresis (DEP), a force which acts on polarizable analytes in the presence of a non-uniform electric fields. This method can achieve high resolution separations with the unique attribute of concentrating, rather than diluting, analytes upon separation. Studies utilizing DEP have manipulated a wide range of analytes including various cell types, proteins, DNA, and viruses. These analytes range from approximately 50 nm to 1 µm in size. Many of the currently-utilized techniques for assessing these analytes are time intensive, cost prohibitive, and require specialized equipment and technical skills. The work presented in this dissertation focuses on developing and utilizing insulator-based dielectrophoresis (iDEP) to probe a wide range of analytes; where the intrinsic properties of an analyte will determine its behavior in a microchannel. This is based on the analyte’s interactions with the electrokinetic and dielectrophoretic forces present. Novel applications of this technique to probe the biophysical difference(s) between serovars of the foodborne pathogen, Listeria monocytogenes, and surface modified Escherichia coli, are investigated. Both of these applications demonstrate the capabilities of iDEP to achieve high resolution separations and probe slight changes in the biophysical properties of an analyte of interest. To improve upon existing iDEP strategies a novel insulator design which streamlines analytes in an iDEP device while still achieving the desirable forces for separation is developed, fabricated, and tested. Finally, pioneering work to develop an iDEP device capable of manipulating larger analytes, which range in size 10-250 µm, is presented. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2018

It has been repeatedly proven that cell therapies can address many current unmet clinical treatment needs and also improve on current treatment options for various diseases, from neurological disorders to bone repair (Rosset et al. 2014; Corey et al. 2017). Though the potential of cell therapies has been demonstrated at a relatively small scale, the realisation of bringing cell based treatments to a larger market is hindered by the complexity of the product along with safety concerned and high production cost. Safety concerns can be informed with more in-depth analytical analysis of the product, however this in turn increase the costs involved in producing a cell therapy (Davie et al. 2012). Consequently the cost of analytical techniques also needs to be reduced, to address this need the area of microfluidic based bioanalytics holds much promise (Titmarsh et al. 2014). The culturing of human mesenchymal stem cells (hMSC) was used as a proof of concept model to demonstrate where improved bioanalytical and bioassay methods could be utilised in the production of cell therapies. Cells from four donors were cultured under three different oxygen environments and the conditioned medium assessed for pro-angiogenic capabilities using a tube formation bioassay and a proportion of the cytokine secretome profile measured using Luminex technology. Thorough secretome analysis it was shown that predicting cytokine levels based solely on the donor was not possible as the handling of the cells also had an influence on the secretome profile. The donor expression profiles did not behave in the same manner across all oxygen environments, for example in some donors IL-8 levels increased per cell at lower oxygen where as other donors showed a decrease per cell. While the tube formation assay showed some differences between donors in pro-angiogenic capabilities it also highlights the challenges with interpreting large data sets. The feasibility of using a microcapillary film (MCF) based enzyme-linked immunosorbent assay (ELISA) to detected two relevant cytokines, IL-8 and hepatocyte growth factor (HGF) was investigated. Following on from this work the development of a combined MCF ELISA assay with hMSC cell culture to produce a fully closed cell screening system was initiated. It was shown that it was feasible to measure IL-8 and HGF using the MCF ELISA platform but further work would need to be done to make the system more compatible with the manufacturing environment. In order to adapt the MCF to also be an hMSC culture platform the first challenge was to functionalise the Fluorinated Ethylene Propylene (FEP) surface of the MCF. It was concluded that a poly (vinyl- alcohol) (PVA) and gelatin mixture produced a homogenous coating to which a consistent level of hMSC would attach. This work was carried out on a flat surface; therefore steps were taken to adapt this knowledge into the MCF, while there was evidence of hMSCs present inside the MCF more work will need to be done to bring this concept to an established platform.

Orientador: Lauro Tatsuo Kubota / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-23T23:55:15Z (GMT). No. of bitstreams: 1 Miranda_BarbaraSantosde_D.pdf: 3761472 bytes, checksum: d04db9862f7022a5bea49d756efbfdbc (MD5) Previous issue date: 2013 / Resumo: Este trabalho apresenta o desenvolvimento de dois sensores distintos que através da aplicação de nanomateriais em seus sistemas apresentam uma melhora no desempenho. Com o objetivo de estabilizar a fase alfa do hidróxido de níquel, foi proposta uma nova síntese que resultou em um novo material de hidróxido de níquel e nanopartículas de ouro. O do hidróxido de níquel se apresentou com a estrutura alfa desejada, a estrutura e morfologia das nanopartículas de ouro foram preservadas. O material híbrido se apresenta nanoestruturado e sem separação de fases. Sugere-se que este novo material seja formado como um nanocompósito onde as nanopartículas de ouro formam a matriz e o hidróxido de níquel recobre a superfície. A estabilidade do novo material é bem superior que a do hidróxido de níquel puro, quedas de corrente após 50 ciclos consecutivos de 6% contra 50% respectivamente. A atividade eletrocatalítica deste novo nanomaterial foi investigada frente à glicose e a constante eletrocatalítica obtida para o nanocompósito foi cerca de 7 vezes maior que para o hidróxido de níquel puro. A sensibilidade do eletrodo modificado com a-Ni(OH)2/AuNP se manteve similar aos da literatura. O segundo sensor estudado foi a aplicação de nanopartículas fluorescentes como marcadores do imunosensor para a detecção precoce do esporo do fungo da ferrugem asiática da soja. As nanopartículas fluorescentes permitiram alcancar um baixo limite de detecção, 2.2 ng/mL, o menor encontrado na literatura. Além disso, foi investigado outros parâmetros para o desenvolvimento de um dispositivo point-of-care, como o melhor substrato para reter o analito, a membrana de nitrocelulose, se apresentou com as melhores propriedades frente as alternativas. Ainda mais, o dispositivo foi construido para que possa ser utilizado por pessoas não treinadas no campo, em um tempo de análise menor que ELISA e PCR, sem o uso de equipamento caros e complicados, usando somente uma lâmpada de UV simples como fonte de excitação e a visualização do sinal a olho nu com um limite de detecção de apenas 300 esporos, o que e ainda dez vezes mais baixo que o atual teste comercial. / Abstract: This work presents the development of two distinct sensors that have shown great improvements in their performance trough nanoparticle application in their systems. The first study aims to stabilize the nickel hydroxide alpha structure for future carbohydrate detection. We proposed a new synthesis, which resulted in a nickel hydroxide and gold nanoparticle hybrid material. The new material has the expected nickel hydroxide alpha structure, maintains gold nanoparticle¿s structure and morphology and allows a simple electrode modification. We suggest that the new material is a nanocomposite where gold nanoparticles are the matrix while the nickel hydroxide cover the surface. The new material has higher stability properties than the pure nickel hydroxide, after 50 cycles the current decreased 6 and 50% respectively. In addition, an improvement was observed in the catalytic constant, approximately 7 times bigger than plain nickel hydroxide. Although the new material showed these good improvements, the electrode sensitivity did not differ from other studies in the literature. The second study presented comprehends the application of fluorescent nanoparticles as markers of an immunosensor for early diagnosis of Asian soybean rust spore. The use of these nanoparticles resulted in a very low limit detection sensor, 2.2 ng/mL, the lowest ever found in the literature. Moreover, others parameters were investigated in order to develop a point-of-care device, as the substrate to retain the analyte for the assay. Furthermore, the device was built in order to be used by the farmer himself, in loco, fast, without expensive equipment, a UV lamp as an excitation source and the signal is visible to naked eye. The visual detection limit is around 300 spores, which is tenfold lower than the available commercial kit. / Doutorado / Físico-Química / Doutora em Ciências

The data presented in this thesis showcases the investigation of various aerosol types and the role they play in the hydrological system and global climate models. Long-range transport aerosols, including atmospheric soot, mineral dust, and ammonium sulfate, in addition to near-site sources such as secondary organic aerosols (SOAs), sea spray, aliphatic hydrocarbons, and other organics, are prioritized in the analysis of two separate remote field studies. Each of these campaigns revealed the juxtaposition between dry summer months and wet winter months, and the connection between seasonal variability and sample collection. Two spectromicroscopic techniques were used to elucidate chemical composition, morphology and size of particles. Quantification of C, N, and O was performed using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure (STXM/NEXAFS) and used to generate organic volume fractions and to provide mixing state parameters and diversity measurements. This was followed by utilizing scanning electron microscopy in the energy dispersive X-ray (SEM/EDX) mode on the same particle sets to characterize 11 heavier elements: Na, Mg, P, S, Cl, K, Ca, Mn, Fe, Ni, and Zn.

Metallische Nanostäbe mit einer Länge im Mikrometer-Bereich wirken als Antennen für infrarotes Licht: Indem unter Lichteinfall eine kollektive Schwingung der Leitungselektronen angeregt wird (ein sogenanntes Plasmon), wird das elektrische Feld an den Stabenden stark konzentriert. Besonders starke Feldkonzentrationen treten auf, wenn zwei Antennenarme durch eine schmale Lücke getrennt sind (Dimerantenne). Somit können die Antennen Licht-Materie-Wechselwirkungen -- wie beispielsweise die Absorption infraroten Lichtes von Molekülen -- verstärken. Dieses als oberflächenverstärkte Infrarotabsorption (SEIRA) bezeichnete Phänomen ist sehr nützlich, um Signale in der Infrarotspektroskopie zu verstärken. Diese Arbeit widmet sich der effizienten Herstellung von metallischen Nanostäben für SEIRA. Im ersten Schwerpunktthema werden Dimerantennen, die per Elektronenstrahllithographie (EBL) hergestellt wurden und eine auflösungsbegrenzte Lücke aufweisen, durch eine photochemische Reduktion von Metallsalzkomplexen nachträglich vergrößert. Dadurch verringert sich die Lückengröße und erreicht Werte deutlich unter der Auflösungsgrenze der EBL. Es wird gezeigt, dass diese photochemische Abscheidung die IR-optischen Eigenschaften der Dimerantennen durch plasmonische Kopplung entscheidend verändert. Zudem steigt die Infrarotabsorption von in der Lücke befindlichen Molekülen mit sinkender Lückengröße. Im zweiten Schwerpunktthema liegt der Fokus auf der günstigen Fabrikation einer Vielzahl von IR-Antennen in einem parallelen Prozess. Dabei werden poröse Template aus anodisiertem Aluminiumoxid (AAO) als Negativ für die herzustellenden Metallstäbe benutzt. Es wird zuerst gezeigt, dass die Poren des Templates durch die photochemische Reduktion von Goldsalzkomplexen befüllt werden können. Für eine gezielte Einstellung der Stäbchenlänge und die Generierung einer nanoskaligen Lücke wird weiterhin die elektrochemische Befüllung der Template untersucht. Die hiermit hergestellten IR-Antennen werden vereinzelt, auf ein Substrat aufgetragen und hinsichtlich ihrer Struktur und ihrer IR-optischen Eigenschaften charakterisiert. Die Vor- und Nachteile der untersuchten Herstellungsmethoden und ihre Eignung für die Fabrikation von IR-Antennen für SEIRA werden diskutiert. / Metallic nanorods with lengths in the micrometer regime act as antennas for infrared light: As incident light excites a collective oscillation of the conduction electrons (a so-called plasmon), the electric field is concentrated at the rod ends. In case two antenna arms are separated by a small gap (dimer antenna), a particularly high field concentration occurs. Thereby the antennas are capable of enhancing light-matter-interaction -- for example the absorption of infrared light by molecules. This phenomenon, termed as surface enhanced infrared absorption (SEIRA), is very useful to enhance absorption signals in infrared spectroscopy. This thesis attends to the efficient fabrication of metallic nanorods for SEIRA. The first topic in focus is the manipulation of dimer antennas fabricated by electron beam lithography (EBL), featuring a gap of resolution-limited size. By applying a photochemical reduction of metal salt complexes in solution, the dimer arms are subsequently enlarged. Thereby the gap size is reduced and reaches values clearly below the resolution limit of EBL. It is shown that the IR optical properties of dimer antennas dramatically change during photochemical metal deposition. This is due to plasmonic coupling. Additionally, the absorption of infrared light by molecules located in the gap increases with decreasing gap size. The second topic in focus is the cheap fabrication of a large number of IR antennas in a parallel process. Here, porous templates of anodized aluminum oxide (AAO) are used as a negative for the metal rods to be fabricated. Firstly, it is shown that the pores of the template can be filled by photochemical reduction of gold salt complexes. For a targeted adjustment of the rod lengths and the generation of a nanoscale gap, secondly, the electrochemical filling of acsu AAO is investigated. The IR antennas prepared by this method are extracted from the template, transferred to a substrate, and individually characterized in terms of their structure and IR optical properties. Advantages and drawbacks of the fabrication methods investigated in this work as well as their applicability to the fabrication of IR antennas for SEIRA are being discussed.

Metallische Nanostäbe mit einer Länge im Mikrometer-Bereich wirken als Antennen für infrarotes Licht: Indem unter Lichteinfall eine kollektive Schwingung der Leitungselektronen angeregt wird (ein sogenanntes Plasmon), wird das elektrische Feld an den Stabenden stark konzentriert. Besonders starke Feldkonzentrationen treten auf, wenn zwei Antennenarme durch eine schmale Lücke getrennt sind (Dimerantenne). Somit können die Antennen Licht-Materie-Wechselwirkungen -- wie beispielsweise die Absorption infraroten Lichtes von Molekülen -- verstärken. Dieses als oberflächenverstärkte Infrarotabsorption (SEIRA) bezeichnete Phänomen ist sehr nützlich, um Signale in der Infrarotspektroskopie zu verstärken. Diese Arbeit widmet sich der effizienten Herstellung von metallischen Nanostäben für SEIRA. Im ersten Schwerpunktthema werden Dimerantennen, die per Elektronenstrahllithographie (EBL) hergestellt wurden und eine auflösungsbegrenzte Lücke aufweisen, durch eine photochemische Reduktion von Metallsalzkomplexen nachträglich vergrößert. Dadurch verringert sich die Lückengröße und erreicht Werte deutlich unter der Auflösungsgrenze der EBL. Es wird gezeigt, dass diese photochemische Abscheidung die IR-optischen Eigenschaften der Dimerantennen durch plasmonische Kopplung entscheidend verändert. Zudem steigt die Infrarotabsorption von in der Lücke befindlichen Molekülen mit sinkender Lückengröße. Im zweiten Schwerpunktthema liegt der Fokus auf der günstigen Fabrikation einer Vielzahl von IR-Antennen in einem parallelen Prozess. Dabei werden poröse Template aus anodisiertem Aluminiumoxid (AAO) als Negativ für die herzustellenden Metallstäbe benutzt. Es wird zuerst gezeigt, dass die Poren des Templates durch die photochemische Reduktion von Goldsalzkomplexen befüllt werden können. Für eine gezielte Einstellung der Stäbchenlänge und die Generierung einer nanoskaligen Lücke wird weiterhin die elektrochemische Befüllung der Template untersucht. Die hiermit hergestellten IR-Antennen werden vereinzelt, auf ein Substrat aufgetragen und hinsichtlich ihrer Struktur und ihrer IR-optischen Eigenschaften charakterisiert. Die Vor- und Nachteile der untersuchten Herstellungsmethoden und ihre Eignung für die Fabrikation von IR-Antennen für SEIRA werden diskutiert. / Metallic nanorods with lengths in the micrometer regime act as antennas for infrared light: As incident light excites a collective oscillation of the conduction electrons (a so-called plasmon), the electric field is concentrated at the rod ends. In case two antenna arms are separated by a small gap (dimer antenna), a particularly high field concentration occurs. Thereby the antennas are capable of enhancing light-matter-interaction -- for example the absorption of infrared light by molecules. This phenomenon, termed as surface enhanced infrared absorption (SEIRA), is very useful to enhance absorption signals in infrared spectroscopy. This thesis attends to the efficient fabrication of metallic nanorods for SEIRA. The first topic in focus is the manipulation of dimer antennas fabricated by electron beam lithography (EBL), featuring a gap of resolution-limited size. By applying a photochemical reduction of metal salt complexes in solution, the dimer arms are subsequently enlarged. Thereby the gap size is reduced and reaches values clearly below the resolution limit of EBL. It is shown that the IR optical properties of dimer antennas dramatically change during photochemical metal deposition. This is due to plasmonic coupling. Additionally, the absorption of infrared light by molecules located in the gap increases with decreasing gap size. The second topic in focus is the cheap fabrication of a large number of IR antennas in a parallel process. Here, porous templates of anodized aluminum oxide (AAO) are used as a negative for the metal rods to be fabricated. Firstly, it is shown that the pores of the template can be filled by photochemical reduction of gold salt complexes. For a targeted adjustment of the rod lengths and the generation of a nanoscale gap, secondly, the electrochemical filling of acsu AAO is investigated. The IR antennas prepared by this method are extracted from the template, transferred to a substrate, and individually characterized in terms of their structure and IR optical properties. Advantages and drawbacks of the fabrication methods investigated in this work as well as their applicability to the fabrication of IR antennas for SEIRA are being discussed.

[ES] Los sistemas CRISPR-Cas se basan en un mecanismo del sistema inmune adaptativo que se encuentra en bacterias y arqueas. Funcionan utilizando endonucleasas guiadas por ARN (proteínas Cas) para localizar y reconocer secuencias específicas de ácidos nucleicos. Los sistemas CRISPR-Cas son revolucionarios en el campo de la ingeniería genética, permitiendo la edición específica del genoma, ensayos de regulación genética y, desarrolladas en los últimos años, aplicaciones de diagnóstico. Los métodos de detección de ácidos nucleicos son la técnica de diagnóstico de referencia en la clínica debido a su alta sensibilidad y especificidad. Sin embargo, de cara al futuro, debemos desarrollar métodos versátiles de detección de virus que permitan diagnósticos rápidos y fiables, que superen las limitaciones de las técnicas actuales y puedan usarse fácilmente fuera del laboratorio para aplicaciones en puntos de atención (POC). Los sistemas CRISPR-Cas se han reconvertido en herramientas de diagnóstico de ácidos nucleicos gracias a la capacidad de algunas proteínas Cas de realizar cortes colaterales no específicos al reconocer su diana. Nuestro objetivo es ampliar el conjunto de herramientas de diagnóstico CRISPR-Cas mediante el desarrollo de una nueva estrategia de detección de ácidos nucleicos basada en CRISPR-Cas9, cuyo modo de acción se basa en el desplazamiento de hebra en lugar de en la catálisis colateral. Demostramos que los amplicones de ADN del SARS-CoV-2 generados a partir de muestras de pacientes pueden detectarse con CRISPR-Cas9. También demostramos la capacidad de realizar la detección simultánea de diferentes amplicones de ADN con la misma nucleasa, ya sea para identificar diferentes regiones de SARS-CoV-2 o diferentes virus respiratorios. Para avanzar hacia aplicaciones POC, acoplamos el paso de preamplificación isotérmica con oligos biotinilados para producir amplicones marcados. Cuando se combina con CRISPR-Cas9 y sondas marcadas con FAM, esto permite la visualización colorimétrica de la detección mediante ensayos de flujo lateral (LFA) en tiras disponibles en el mercado. La lectura colorimétrica permite la interpretación de los resultados a simple vista, superando la necesidad de un fluorímetro. Detectamos con éxito SARS-CoV-2 a partir de muestras de pacientes en la configuración LFA, y cuando se combinó con RT-RPA multiplexado, se logró la detección de dos regiones distintas del virus en una sola prueba. Además, la ausencia de actividad colateral en nuestra metodología permite el procesamiento de secuencias posteriores adicionales. Por lo tanto, también pretendemos explorar la capacidad de integración de señales de nuestro método de detección basado en CRISPR-Cas9. Demostramos que diseños de circuitos lógicos de ADN pueden procesar diferentes señales de SARS-CoV-2 detectadas por los complejos CRISPR. También nos propusimos mejorar nuestro sistema CRISPR-Cas9 para detectar tanto proteínas como ácidos nucleicos. Nos propusimos diseñar un ARN guía condicional que respondiera a la presencia de la proteína spike del SARS-CoV-2. Para ello, insertamos un aptámero en el ARN guía para bloquear la actividad de Cas9 en ausencia de la proteína. En presencia de la proteína spike, la interacción aptámero-proteína hace que el motivo de bloqueo sufra un cambio conformacional, liberando el ARN guía y activando Cas9. Aunque logramos con éxito el escenario de bloqueo utilizando las secuencias reguladoras, es necesario seguir trabajando para identificar una secuencia que pueda inducir el cambio conformacional específico necesario para restaurar la actividad de Cas9 en presencia de la proteína spike. En conjunto, esta plataforma de diagnóstico CRISPR-Cas9 permite una detección multiplexada en un solo tubo, complementando los métodos existentes basados en CRISPR, y ofreciendo un sistema extensible para aplicaciones en diagnóstico en el punto de atención y biocomputación. / [CA] Els sistemes CRISPR-Cas es basen en un mecanisme del sistema immunitari adaptatiu que es troba en bacteris i arqueus. Funcionen utilitzant endonucleases guiades per ARN (proteïnes Cas) per tal de dirigir-se i reconéixer seqüències específiques d'àcids nucleics. Els sistemes CRISPR-Cas siguen revolucionaris en el camp de l'enginyeria genètica, permetent l'edició específica del genoma, assajos de regulació gènica i, desenvolupades en els darrers anys, aplicacions de diagnòstic. Els mètodes de detecció d'àcids nucleics són la tècnica de diagnòstic de referència a la clínica degut a la seua alta sensibilitat i especificitat. No obstant, de cara al futur, hem de desenvolupar mètodes versàtils de detecció de virus que permeten diagnòstics ràpids i fiables, que superen les limitacions de les tècniques actuals i puguen utilitzar-se fàcilment fora del laboratori per a aplicacions en punts d'atenció (POC). Els sistemes CRISPR-Cas han estat reorientats com a eines de diagnòstic d'àcids nucleics, fet possible per la capacitat d'algunes proteïnes Cas de realitzar un tall col·lateral no específic en reconèixer un objectiu. El nostre objectiu és ampliar el conjunt d'eines de diagnòstic CRISPR-Cas desenvolupant una nova estratègia de detecció d'àcids nucleics basada en CRISPR-Cas9, el mode d'acció del qual es basa en el desplaçament de cadena en lloc de la catàlisi col·lateral. Mostrem que es poden detectar amplicons de DNA de SARS-CoV-2 generats a partir de mostres de pacients amb CRISPR-Cas9. També demostrem la capacitat de realitzar la detecció simultània de diferents amplicons de DNA amb la mateixa nucleasa, ja siga per identificar diferents regions de SARS-CoV-2 o diferents virus respiratoris. Per avançar cap a aplicacions de punt d'atenció (POC), vam combinar el pas de preamplificació isotèrmica amb oligos biotinilats per produir amplicons etiquetats. Quan es combinen amb l'orientació CRISPR-Cas9 i sondes etiquetades amb FAM, això permet la visualització colorimètrica de la detecció mitjançant assajos de flux lateral (LFA) en tires comercials disponibles. La lectura colorimètrica permet la interpretació dels resultats a simple vista, superant la necessitat d'un fluorímetre. Vam detectar amb èxit el SARS-CoV-2 a partir de mostres de pacients en el sistema LFA, i quan es va combinar amb RT-RPA multiplexada, es va aconseguir la detecció de dues regions diferents del virus en una sola prova. A més, l'absència d'activitat col·lateral en la nostra metodologia permet el processament de seqüències addicionals. Per tant, també ens proposem explorar la capacitat d'integració de senyals del nostre mètode de detecció basat en CRISPR-Cas9. Demostrem que els circuits lògics d'ADN dissenyats poden processar diferents senyals de SARS-CoV-2 detectats pels complexos CRISPR. També vam intentar millorar el nostre sistema CRISPR-Cas9 per detectar tant proteïnes com àcids nucleics. Ens vam proposar dissenyar un ARN guia condicional que respon a la presència de la proteïna spike del SARS-CoV-2. Per aconseguir-ho, vam inserir una seqüència d'aptàmer dins de l'ARN guia per bloquejar l'activitat de Cas9 en absència de la proteïna. En presència de la proteïna spike, la interacció aptàmer-proteïna fa que el motiu de bloqueig experimente un canvi conformacional, alliberant l'ARN guia i activant Cas9. Tot i que vam aconseguir amb èxit el bloqueig utilitzant les seqüències reguladores, es necessita més treball per identificar una seqüència que puga induir el canvi conformacional específic necessari per restaurar l'activitat de Cas9 en presència de la proteïna spike. Col·lectivament, aquesta plataforma de diagnòstic CRISPR-Cas9 permet una detecció multiplexada en un sol tub, complementant els mètodes existents basats en CRISPR i oferint un sistema extensible per a aplicacions en diagnòstics de punt d'atenció i biocomputació. / [EN] CRISPR-Cas systems are based on an adaptive immune system mechanism found in bacteria and archaea. They function using RNA-guided endonucleases (Cas proteins), to target and recognize specific nucleic acid sequences. CRISPR-Cas systems are revolutionary in the field of genetic engineering, enabling specific genome editing, gene regulation assays and, developed in recent years, diagnostic applications. Nucleic acid detection methods are the gold-standard diagnostic technique in the clinic due to their high sensitivity and specificity. However, going forward, we must develop versatile virus detection methods that enable fast and reliable diagnostics and that can overcome the limitations of the current techniques and can be easily used outside the laboratory for point-of-care (POC) applications. CRISPR-Cas systems have been repurposed as nucleic acid diagnostic tools made possible by the ability of some Cas proteins to perform non-specific collateral cleavage upon target recognition. We aim to expand the CRISPR-Cas diagnostic toolkit by developing a novel nucleic acid detection strategy based on CRISPR-Cas9, whose mode of action relies on strand displacement rather than on collateral catalysis. We show that SARS-CoV-2 DNA amplicons generated from patient samples can be detected with CRISPR-Cas9. We also demonstrate the ability to perform simultaneous detection of different DNA amplicons with the same nuclease, either to identify different SARS-CoV-2 regions or different respiratory viruses. To advance toward POC applications, we coupled the isothermal preamplification step with biotinylated oligos to produce labelled amplicons. When combined with CRISPR-Cas9 targeting and FAM-labelled probes, this allows for colorimetric visualization of detection using lateral flow assays (LFA) on commercially available strips. The colorimetric readout enables interpretation of the results with the naked eye, surpassing the need for a fluorimeter. We successfully detected SARS-CoV-2 from patient samples in the LFA setup, and when combined with multiplexed RT-RPA, the detection of two distinct regions of the virus was achieved in a single test. Furthermore, the absence of collateral activity in our methodology allows for the processing of additional downstream sequences. Therefore, we also aim to explore the signal integration capability of our CRISPR-Cas9-based detection method. We demonstrate that engineered DNA logic circuits can process different SARS-CoV-2 signals detected by the CRISPR complexes. We also aimed to enhance our CRISPR-Cas9 system to sense both proteins and nucleic acids. We aimed to engineer a conditional guide RNA that responds to the presence of the SARS-CoV-2 spike protein. To achieve this, we inserted an aptamer sequence within the guide RNA to block Cas9 activity in the absence of the protein. Upon the presence of the spike protein, aptamer-protein interaction makes the blocking motif undergo a conformational change, releasing the guide RNA and activating Cas9. While we successfully achieved the blocking scenario using the regulatory sequences, further work is needed to identify a sequence that can induce the specific conformational change required to restore Cas9 activity upon spike protein presence. Collectively, this CRISPR-Cas9 diagnostic platform allows a multiplexed detection in a single tube, complementing the existing CRISPR-based methods, and offering an extensible system for applications in point-of-care diagnostics and biocomputing. / This work was supported by a predoctoral fellowship from the Spanish Ministry of Science and Innovation (PRE2019-088531). / Márquez Costa, R. (2024). Engineering of CRISPR-Cas9-Based Systems for Diagnostics and Biocomputing [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/210634