The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.

The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.

Submitted by Priscila Nascimento (pnascimento@icict.fiocruz.br) on 2012-11-29T17:53:07Z No. of bitstreams: 1 ana-rodrigues-de-andrade.pdf: 2209967 bytes, checksum: daf5f7b7ad34996e5a40131114f4b681 (MD5) / Made available in DSpace on 2012-11-29T17:53:07Z (GMT). No. of bitstreams: 1 ana-rodrigues-de-andrade.pdf: 2209967 bytes, checksum: daf5f7b7ad34996e5a40131114f4b681 (MD5) Previous issue date: 2011 / Fundação Oswaldo Cruz. Instituto de Tecnologia em Imunobiológicos. Rio de Janeiro, RJ, Brasil. / A eritropoetina é o hormônio responsável pela regulação da produção de células vermelhas. A eritropoetina humana recombinante (rhEPO) produzida em laboratório e usada como medicamento pode apresentar as isoformas alfa e beta, chamadas de alfaepoetina e betaepoetina humana recombinante. O tratamento com rhEPO melhora bastante a vida de pacientes anêmicos e/ou em diálise, reduzindo a necessidade de transfusão de sangue. A grande demanda por este biofármaco justifica o esforço de pesquisa não só para conhecimento de seus mecanismos de ação e desenvolvimento de processos de produção, como também para controle da qualidade do produto. É de grande importância o desenvolvimento de métodos de análise que diminuam a margem de erro e aumentem a precisão e a confiabilidade dos resultados, além de reduzir o tempo de liberação para o mercado. O ensaio de determinação da potência da alfaepoetina humana recombinante produzida por Bio-Manguinhos é realizado pelo método de camundongos normocitêmicos, com contagem de reticulócitos por microscopia. Estemétodo de contagem é demorado, pouco preciso e desgastante para o analista. O objetivo deste trabalho é estudar o uso do método de citometria de fluxo na contagem de reticulócitos para o ensaio de potência da alfaepoetina humana recombinante. Visando a implantação do método no Departamento de Controle de Qualidade (DEQUA) de Bio-Manguinhos, o desenvolvimento deste trabalho teve também como objetivo comparar a sua eficácia em relação aoprocesso atualmente utilizado, e a realizar os testes necessários à sua validação. Os camundongos foram inoculados com três doses diferentes de amostra ou material de referência e os reticulócitos presentes no sangue coletado foram marcados com o corante fluorescente laranja de tiazol (Retic-COUNT). Os reticulócitos foram contados em citômetro de fluxo FACSCalibur e seu percentual foi utilizadopara a determinação da potência de acordo com os cálculos da Farmacopéia Européia 6ª edição. Para a comparação entre os métodos, vinte lotes de alfaepoetina humana recombinante produzidos por Bio-Manguinhos tiveram sua potência determinada pela contagem de reticulócitos por citometria e microscopia. Para a determinação da repetitividade e da precisão intermediária, foi utilizado um único lote de alfaepoetina humana recombinante. Para avaliar a concordância entre os métodos de citometria de fluxo e microscopia, foi utilizado o teste estatístico de Bland-Altman, com comparação dos vinte resultados obtidoscom os mesmo lotes, analisados a partir das mesmas amostras de sangue. Os resultados apresentaram boa repetitividade e precisão intermediária e mostraram que os métodos são equivalentes no que diz respeitoà determinação da potencia da rhEPO produzida por Bio-Manguinhos. No entanto, em funçãoda alta probabilidade de erros associados ao método de microscopia, a introdução da citometria de fluxo mostra-se uma alternativa bastante promissora para suprir a demanda de testes com precisão, reprodutibilidade e maior velocidade de liberação de lotes. / Erythropoietin is the hormone responsible for the regulation of the red cells’ production. The recombinant human erythropoietin (rhEPO) produced in laboratory and used as a drug exists in the alpha and beta isoforms, called alpha epoietin and beta epoietin. The treatment with rhEPO improves the life of anemic patients and/or on dialysis, reducing the need for blood transfusion. The high demand for this biopharmaceutical product justifies the research effort not only for the knowledge of its mechanisms of action and development of production processes, but also for the product quality control. The development of quality control methods able to reduce errors and increase the accuracy and the reliability of the results, along with a reduction in the release timeto the market, is of great importance. The assay to determine the biological activity of the recombinant human alpha epoietin produced in Bio-Manguinhos is performed bythe normocythaemic mice method and reticulocyte counting by microscopy. This counting method is time consuming, imprecise and stressful to the analyst. The present study aimed to study the use of the flow cytometric method for reticulocyte counting in the biological activity assay for the human alpha epoietin. Intending to implement this new method in the Quality Control Department of Bio-Manguinhos, this work also compared its effectiveness with the currently used method, and the tests required to its validation were performed. The mice were inoculated with three different dosesof sample and reference material, and the reticulocytes on the collected blood were stained with the fluorescent dye thiazole orange (Retic-COUNT). The reticulocytes were counted in a FACSCalibur flow cytometer and their percentage was used for the biological activity determination in accordance with the European Pharmacopoeia 6 th edition. To compare the methods, the biological activity of twenty batches of recombinant human alpha epoetin produced by Bio-Manguinhos was determined trough both cytometry and microscopy. Tothe determination of repeatability and intermediate precision, only a single batch of recombinant human alpha epoetin was used. For the evaluation of agreement between both methods, the Bland-Altman test was used to the compare the twenty results obtained from the same batches, analyzed from the same blood samples. The results showed good repeatability and intermediate precision and indicated that the two methods are equivalent when it concerns thedetermination of the rhEPO biological activity. However, due to the high probability of errors associated with the microscopy method, the introduction of the flow cytometry method seems to be a promising alternative to meet the demand for analyses with precise and reproducible results, along with a good speed in releasing batches for the market.

Im ersten Teil der Arbeit wurde die Verwendung von Präkursor microRNA-21(pre-miR21)-spezifischen Peptidnukleinsäure(PNA)-Sonden zur Inhibierung der Dicer-vermittelnden miRNA-Reifung untersucht. Im Gegensatz zur Arbeitshypothese wurde bei der Behandlung von Zellen mit den pre-miR21-spezifischen PNA-Sonden jedoch keine Änderung des miR-21 Niveau beobachtet. Um die Hybridisierung der Sonde an die Zielsequenz nachzuweisen, wurden fluorogene Hybridisierungssonden zur erzwungenen Interkalation (FIT-Sonden), unter Verwendung des Interkalationsfarbstoffes Thiazolorange (TO), entwickelt. Wie vorläufige Ergebnisse zeigen, könnte die TO-PNA Sonde für die Unterscheidung von Zellen mit hohem miR-21-Gehalt nützlich sein, aber eine weitere Verbesserung der Sonde ist noch erforderlich. Im nächsten Teil der Arbeit wurden neuartige FIT-Sonden für die Analyse der Dicer-vermittelnden miR-21-Reifung entwickelt. Um die gleichzeitige Detektion der entstehenden pre-miR21 und der antisense miR-21 (as-miR21) in Echtzeit zu ermöglichen, wurden die Verwendung von spektral unterscheidbaren FIT-Sonden auf Quinolinblau(QB)-und TO-Basis getestet. Das entwickelte Sonden-Paar ermöglichte die Analyse der rhDicer-Reaktion. Dabei wurde entdeckt, dass die rhDicer-Reaktion an der in vitro transkribierten pre-miR21 unspezifisch spaltet. Zusätzlich wies die kürze as-miR21 spezifische TO-Sonde (7nt) eine Sensitivität gegenüber der Anwesenheit des Ago-2 Proteins auf. In der Zukunft könnten die entwickelten Sonden für schnelle in vitro Screenings neuer Dicer-und Ago-2-Inhibitoren angewendet werden. Im zweiten Teil der Dissertation wurde die Verwendung von niedermolekularen Inhibitoren (small molecular inhibitors, SMIs) getestet. Zusammenfassend könnten die zwei identifizierten SMIs für die Inhibierung der miR-122-Reifung genutzt werden, allerdings bleibt die Spezifität der SMIs fraglich und mögliche off-target-Effekte können nicht ausgeschlossen werden. / MicroRNAs (miRNAs) represent small non-coding RNA molecules that mostly negatively regulate gene expression. To yield mature miRNAs, primary miRNA precursors go through two consequent cleavages by Drosha and Dicer RNAse. This work describes the development of tools for inhibition und monitoring the dicer-mediated miRNA processing. Here, peptide nucleic acid (PNA) based probes, targeting the precursor miR-21 (pre-miR21), were designed for inhibition the dicer-mediated miR-21 maturation. In contrast, no change in miR-21 level was observed after cell treatment with the pre-miR21 specific PNA probes. To detect the probe/target hybridization state, the fluorogenic forced intercalation (FIT) PNA probes, bearing thiazole orange dye (TO), were developed. As preliminary results show, the FIT PNA probe might be useful for discrimination of high miR-21 abundant cells, but further probe improvement is still required. To monitor the pre-miR21 cleavage, the combination of the two spectrally distinguishable FIT PNA probes, bearing quinoline blue (QB) and TO fluorophore, was developed to allow the rapid and simultaneous detection of pre-miR21 and antisense mature miR-21 (as-miR21). The probe set was successfully used for detection of the modelled dicer reaction. However, the monitoring of rhDicer reaction have revealed that rhDicer cleaves the in vitro transcribed pre-miR21 nonspecifically. Additionally, the short as-miR21 specific TO PNA probe (7nt) was responsive to the presence of Ago-2 protein. In future, the developed probes can be applied for the fast in vitro screening of new Dicer and Ago-2 inhibitors. In the second part of this work, an alternative approach, small molecular inhibitors (SMIs), was tested. Two identified pre-miR122-targeting SMIs might be used for inhibition of the miR-122 maturation, although, a specificity of these SMIs remains questionable and possible off target effects cannot be excluded.