Die Verwendung von nukleinsäuretemplatgesteuerten Reaktionen stellt einen innovativen Ansatz zur Therapie von Krankheiten dar, deren Ursprung in einer genetischen Veränderung von Zellen liegt. Im Rahmen der hier vorliegenden Arbeit erfolgte eine Weiterentwicklung der RNA-templatgesteuerten Acyltransferreaktion nach Seitz et al. hinsichtlich des Aufbaus von aromatischen Amidbindungen, wie sie in vielen niedermolekularen Wirkstoffen vorkommen. Als Modellverbindungen dienten die Bcr-Abl-Tyrosinkinaseinhibitoren Nilotinib, Ponatinib und GZD824, die durch zentrale Benzanilidmotive charakterisiert sind und zur Therapie der chronischen myeloischen Leukämie eingesetzt werden. Das konzipierte Reaktionssystem beruht auf dem Mechanismus der nativen chemischen Ligation, weswegen die Bcr-Abl-Inhibitoren durch die Einführung einer Thiolgruppe modifiziert werden mussten. Es wurde gezeigt, dass diese Modifikation in den meisten Fällen nur zu einer geringen Beeinträchtigung der biologischen Aktivität führt. Der RNA-templatgesteuerte Aufbau der Benzanilidstrukturen konnte sowohl mit PNA- als auch mit DNA-verknüpften Inhibitorfragmenten basierend auf Ponatinib und GZD824 erzielt werden. In Gegenwart eines komplementären RNA-Templats erfolgte die benachbarte Hybridisierung der reaktiven Konjugate, infolgedessen ein Benzoyltransfer von einem thioestermodifizierten Donor auf ein ortho-Mercaptoanilinderivat als Akzeptor stattfand. Mit PNA/PNA-Reaktionssystemen wurde auch in Abwesenheit des RNA-Templats eine signifikante Produktbildung beobachtet, was auf hydrophobe Wechselwirkungen der Konjugate zurückgeführt wurde. Unter Verwendung von DNA/DNA- bzw. PNA/DNA-Konjugatpaaren blieb die templatunabhängige Produktbildung hingegen ausreichend gering. Die entsprechenden Reaktionssysteme wurden hinsichtlich der erzielten Produktausbeuten optimiert, wobei sowohl die Linkerlänge bzw. -struktur der reaktiven Konjugate als auch die Templatarchitektur variiert wurde. / The use of nucleic acid-templated reactions represents an innovative approach to the therapy of diseases that originate in genetic alterations of cells. In this work, the RNA-templated acyl transfer reaction invented by Seitz et al. was extended towards the formation of aromatic amide bonds which occur in a variety of small molecule drugs. The Bcr-Abl tyrosine kinase inhibitors nilotinib, ponatinib, and GZD824 were used as model compounds, as they are characterized by central benzanilide motifs and find application in the treatment of chronic myeloid leukemia. The designed reaction system is based on the mechanism of native chemical ligation which required the modification of the Bcr-Abl inhibitors by introducing a thiol group. It was shown that thiolation affected the biological activity only moderately. The RNA-templated formation of the benzanilide structures was achieved with both PNA- and DNA-linked inhibitor fragments of ponatinib and GZD824. The presence of a complementary RNA template enabled adjacent binding of the reactive conjugates, triggering a rapid benzoyl transfer from a thioester-linked donor to an ortho-mercaptoaniline derivative as an acceptor. With PNA/PNA reaction systems, significant product formation was observed in absence of the RNA template, which was attributed to hydrophobic interactions between the conjugates. However, the template-independent product formation remained low when DNA/DNA or PNA/DNA conjugate pairs were used. The product yields of the corresponding reaction systems were optimized by varying the linker length and structure of the conjugates as well as the template architecture.

Improved diagnosis, prognosis and disease follow-up is a fundamental procedure and a constant challenge in medicine.  Among the different molecular biomarkers, proteins are the essential regulatory component in blood; hence, by developing enhanced specific and sensitive molecular tools will gives great insight into the different processes in disease treatment.  In this thesis, we build on the proximity ligation assay to develop and apply new adaptable methods to facilitate protein detection. In paper I, I present a variant of the proximity ligation assay (we call PLARCA) using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer. PLARCA detected femtomolar levels of these proteins in patient samples, which was considerably below the detection threshold for ELISA. In paper II, we developed and adapted a new method into the in situ PLA methods for detection and identification of extracellular vesicles (EVs) using flow cytometry as readout (a method we call ExoPLA).  We identified five target proteins on the surface of the Evs and using three colors, we identified the EV using flow cytometer. In paper III, we aim to improve the efficiency of in situ PLA by creating and developing new designs and versions of the assay we called Unfold probes Through comparison of detection of protein using in situ PLA versus Unfold probes, we observed considerable decrease in non-specific signals, and also a lower detection threshold. In paper IV, we describe the development of a solid phase proximity extension (sp-PEA) assay for protein detection and quantification. We compared detection of IL-8, TNF-alpha, IL-10 and IL-6 using spPEA and PEA; spPEA demonstrations over 2 orders of magnitudes in the lower detection concentrations by decreased in background noise.

INTRODUÇÃO: Estudos recentes têm demonstrado que ocorre geração normal de trombina na cirrose hepática mesmo nos pacientes com diminuição da atividade de protrombina e plaquetopenia, de forma que a utilidade dos testes convencionais de coagulação em predizer o risco de sangramento associado a procedimentos seria questionável. OBJETIVO: O objetivo principal deste estudo foi avaliar se as alterações dos parâmetros de coagulação influenciam a frequência e gravidade do sangramento por úlcera após ligadura elástica de varizes de esôfago. CASUÍSTICA E MÉTODOS: Neste estudo prospectivo de coorte realizado no período de dois anos, no Hospital das Clínicas da Faculdade de Medicina da USP, foram incluídos 150 pacientes com o diagnóstico de cirrose hepática, encaminhados para realização de ligadura elástica como profilaxia primária (n=45) e secundária (n=105) de sangramento por varizes de esôfago. Os critérios de inclusão foram: a) presença de varizes de esôfago de médio ou grosso calibre; b) idade superior a 18 anos; c) concordância em participar do estudo. Os critérios de exclusão foram: a) doenças pulmonares e cardíacas graves ou síndrome hepatorrenal associada; b) carcinoma hepatocelular avançado; c) insuficiência renal com uremia; d) doenças ou uso de drogas que alteram a coagulação sanguínea. Foram analisados em todos os pacientes: International Normalized Ratio (INR), tempo de tromboplastina parcial ativada e contagem de plaquetas. Em 92 pacientes foram avaliados: atividade do fator V, fator de von Willebrand, fibrinogênio, proteínas C e S, dímero-D e tromboelastografia. Os pacientes foram estratificados de acordo com: a) grau de disfunção hepática, avaliado pela classificação de Child-Pugh [Child A, n=74 (49%); Child B, n=42 (28%); Child C, n=34 (23%)]; b) valores de corte de INR [>1,5 (n=28); 1,5 (n=122)]; e plaquetas [<50x103/mm3(n=18); 50x103/mm3 (n=132)]; c) padrões da tromboelastografia; d) valores e/ou atividade dos fatores pró-coagulantes e anticoagulantes naturais. As sessões de ligadura foram realizadas a cada 2 semanas. Os dados de cada paciente foram registrados até dois meses após erradicação das varizes. RESULTADOS: Onze pacientes apresentaram sangramento por úlcera após LE. Sangramento ocorreu em cinco pacientes com Child A/B (4,3%) e em 6 pacientes com Child C (17%) (p=0,0174 para Child A/B versus Child C). Oito pacientes (7,3%) apresentaram sangramento entre os 110 pacientes com valores de corte tradicionalmente considerados seguros para INR e plaquetas e apenas três (7,5%) entre os 40 pacientes com valores de risco (p=1,0). Dentre os 92 pacientes com testes expandidos de coagulação, o sangramento ocorreu em cinco. Não houve diferença em nenhum dos parâmetros de coagulação incluindo os padrões da tromboelastografia entre os pacientes com e sem sangramento. CONCLUSÕES: O sangramento por úlcera após ligadura elástica de varizes de esôfago foi associado com o grau de disfunção hepática (Child C), mas não com os fatores convencionais ou expandidos da coagulação em pacientes cirróticos sem insuficiência renal ou infecção submetidos à ligadura elástica eletiva. Estes resultados tornam discutível a necessidade de administração profilática de agentes pró-coagulantes previamente a procedimentos invasivos eletivos / BACKGROUND & AIMS. There is controversy over whether coagulation status predicts bleeding caused by ulceration after esophageal varices band ligation (EVL). METHODS: EVL was performed for primary (n=45) or secondary (n=105) prophylaxis in 150 patients with cirrhosis (Child A, n=74 [49%]; Child B, n=42 [28%]; Child C, n=34 [23%]). International Normalized Ratio (INR) and platelet counts (PC) were assessed in all. In 92 patients, levels of factor V, fibrinogen, D-dimer, protein C and protein S, von Willebrand factor and thromboelastography (TEG) were assessed. PC <50x103/mm3 and INR >1.5 were considered high-risk cutoffs for bleeding. Conversely, PC 50x103/mm3 with INR 1.5 were safe cutoffs. RESULTS: Overall, 11 patients (7.3%) had post-EVL ulcer bleeding. Bleeding occurred in 5 patients with Child A/B (4.3%) and 6 patients with Child C (17%) (p=0.0174 for Child A/B versus Child C). Eight patients with bleeding were among the 110 below the cutoff for INR and PC, whereas only 3 of the patients with bleeding were among the 40 patients with purported high-risk values (p=1.0). Among the 92 patients with expanded coagulation tests, bleeding occurred in 5. There was no difference in any of the coagulation parameters, including overall TEG patterns, between patients who did and did not bleed. CONCLUSION: Post-EVL ulcer bleeding was associated with Child C status but not with conventional or expanded coagulation indices in cirrhotic patients without renal failure or infection undergoing elective EVL. These results call into question the common use of prophylactic procoagulants in the elective setting. common use of prophylactic procoagulants in the elective setting

Embora esteja comprovada a superioridade da ligadura elástica sobre a esclerose endoscópica na profilaxia secundária da hemorragia varicosa, ainda há discussão se esta vantagem também é observada no tratamento da fase aguda do sangramento. O presente estudo tem como objetivo comparar os resultados da ligadura elástica com a esclerose endoscópica em pacientes admitidos no Pronto-Socorro (PS) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP) por hemorragia digestiva alta provocada por rotura de varizes de esôfago. Tratase de estudo unicêntrico, prospectivo, com alocação aleatória dos pacientes sem crossover. A fim de se detectar diferença de 20% entre a capacidade de hemostasia de cada um dos métodos, cada grupo deveria ser constituído por 260 pacientes, considerando poder estatístico de 80% e nível de significância inferior a 5%. Após diagnóstico endoscópico de rotura de varizes de esôfago, foi realizado sorteio para inclusão dos pacientes em dois grupos: esclerose endoscópica (EE) x ligadura elástica (LE). A esclerose foi realizada através da injeção intravasal de oleato de etanolamina a 3%, em alíquotas de 5ml, acima e abaixo do ponto de ruptura, respeitando o valor máximo por sessão de 20ml. No grupo LE, procurou-se ligar a variz sobre o ponto de ruptura. Se isto não foi possível, procurou-se ligar todo o tecido varicoso dos 3cm finais do esôfago. Foi utilizado o kit de ligadura MBL-6 e cateter VINF 23 (Cook, E. Tamusssino). As variáveis estudadas foram: a taxa de hemostasia inicial (até 5 dias), recidiva hemorrágica precoce (5 dias a 6 semanas), complicações e mortalidade. De maio de 2005 a maio de 2007, foram admitidos, no PS do HCFMUSP, 480 pacientes com hemorragia digestiva alta (HDA) provocada por hemorragia varicosa esofágica. Destes, 380 foram excluídos pelos seguintes motivos: mais de um tratamento prévio com ligadura ou esclerose (n=180), não randomização (n=85), uso de outra técnica hemostática como adesivo tissular de cianoacrilato (n=62) ou tratamento clínico incompleto no momento do exame endoscópico (n=53). Cem pacientes, 50 no grupo EE e 50 no LE foram incluídos no estudo. Destes, 72 eram homens e 28 mulheres, média de idade 52 anos. Os grupos se mostraram homogêneos quanto ao sexo, idade, Child-Pugh, hemoglobinemia à admissão, presença de choque hipovolêmico e calibre das varizes. Não foram encontradas diferenças estatisticamente significantes entre os grupos com relação ao controle inicial do sangramento (5 dias), ressangramento precoce (5 dias a 6 semanas), complicações e mortalidade (9 no grupo EE e 10 no grupo LE). Ao final de 6 semanas, 36 (80%) pacientes no grupo esclerose e 33 (77%) no grupo ligadura elástica estavam vivos e sem sinais de sangramento. Foi encontrada associação estatisticamente significante entre a classificação de Child-Pugh e mortalidade (p<0,001), que foi de 16% nos graus A ou B e 84% nos pacientes Child-Pugh C. Os resultados obtidos com esta casuística limitada sugerem que EE e a LE são igualmente eficazes no controle da hemorragia varicosa aguda. / Despite the superiority of banding over endoscopic sclerosis for secondary prophylaxis of variceal bleeding, there is still debate if this advantage is also observed for the acute bleeding setting. The study aims to compare band ligation (BL) with endoscopic sclerosis (SCL) in patients admitted to the emergency unit for rupture of esophageal varices. Prospective study carried out in a single center, with random allocation of the patients without crossover. In order to detect a 20% difference between the results of each method, each group should consist of 260 patients, considering an 80% statistical power and level of significance less than 5%. After an endoscopic diagnosis of rupture of esophageal varices, the patients were randomly allocated in two groups: SCL and BL. Sclerosis was performed by ethanolamine oleate intravascular injection, above and below the rupture point (maximum volume of 20 ml). In the BL group, banding was attempted at the point of rupture followed by ligation of the whole variceal tissue of the distal esophagus. Six-shooter® and VINF23® catheter (Cook, W. Salem, USA) were employed. Studied variables were initial failure in control bleeding (5 days), early rebleeding rates (5 days to 6 weeks), complications and mortality. From May 2005 to May 2007, 480 patients with an episode of variceal bleeding were admitted to the emergency room. From them, 380 were excluded because more than one previous treatment with SCL or BL (n=180), non-randomization (n=85), the use of another hemostatic technique such as cyanoacrylate tissular adhesive (n=62) and incomplete clinical treatment (n=53).One hundred patients, 50 in the SCL and 50 in the BL group were included in the study (72 male, 28 female, mean age 52 years). No differences between the groups were detected regarding gender, age, Child-Pugh status, the presence of shock at admission, mean hemoglobin levels and varices size. No statistically significant differences were found between the groups regarding control bleeding (5 days) and early rebleeding rates (5 days to 6 weeks), complications and mortality (9 in the SCL vs. 10 in the BL group). By the end of 6 weeks 36 (80%) patients in the SCL group and 33 (77%) in the EBL group were alive and free of bleeding. A statistically significant association was found between Child-Pugh status and mortality (p<0,001), which was 16% for A and B grades and 84% for grade C patients. The results obtained with this limited number of patients suggest that SCL and BL are equally efficient in the control of acute variceal bleeding.

Viruses are obligate intracellular pathogens. Therefore, their successful replication, at every stage from attachment to assembly and egress, is dependent on host cell functions. The host cell in turn engages mechanisms to counteract virus replication. As a result, viruses have evolved mechanisms to evade these counteracting measures as well as ways to reshape the cellular environment into one that’s favourable for successful replication. Systematic studies offer a platform for unravelling virus-cell interactions and in particular can address three important aspects 1) increase our understanding of basic biology of the virus, 2) identify and characterise novel cellular functions 3) provide important leads for novel targets for antiviral therapy. In this study, I investigated two aspects of virus host interaction; the role of microRNAs (miRNAs) in virus infection and the role of interferon inducible genes in virus infection. Human cytomegalovirus (HCMV) is a β herpes virus that infects humans. HCMV maintains a persistent lifelong infection in the host involving a cycle of latency and reactivation. Infection of healthy individuals with HCMV results in relatively minor symptoms. In contrast, infection of individuals with a compromised immune system, as in the case of organ transplant recipients and AIDS patients, can cause significant morbidity and mortality. In common with other herpes viruses, HCMV expresses multiple small regulatory RNAs called miRNAs. HCMV encodes at least 14 miRNAs. Identifying the targets of these miRNAs will help us understand their functional importance during infection. Recently, a biochemical technique called Cross-Linking, Ligation and Sequencing of Hybrids (CLASH), was developed by Tollervey and colleagues, representing the most advanced systematic technique for the identification of miRNA targets. We adapted this approach to identify high confidence miRNA targets during HCMV infection. However, the protocol was sub-optimal and presented us with technical challenges. Although high quality data sets were not generated, the work was crucial for the establishment of the system which is now generating promising data. Virus-cell interactions can also be elucidated by probing for host factors that are important for virus replication. Type I interferon is a highly effective inhibitor of HCMV replication. Treatment of cells with interferon results in up regulation of multiple effectors known as interferon stimulated genes (ISGs). How these genes block HCMV replication is poorly understood. A library of more than 380 ISG expressing lentiviruses was screened to determine the effects of individual ISGs on HCMV replication. The screen was performed in primary human fibroblast cells and a glioblastoma cell line called U373s. Multiple inhibitory ISGs were identified including well characterised ISGs such as cGAS, STAT2, NOD2, DDX60 and HPSE as well as novel candidates TXNIP, ELF1, FAM46C, MT1H and CHMP5. Five ISGs were identified as HCMV replication enhancers including previously published ISGs BST2 and IFITM1 and novel enhancers ODC1, BCL3 and IL28RA. siRNA screens against top hits demonstrated that STAT2, CPT1A and cGAS are dominant inhibitory factors during HCMV infection and knockdown of these genes can partially rescue HCMV replication following interferon treatment. Finally, using a corresponding rhesus ISG library we show that rhesus SAMHD1 effectively inhibits HCMV replication while human SAMHD1 has no effect, suggesting that HCMV expresses a species-specific inhibitor of SAMHD1. This study defines interferon stimulated pathways important for HCMV replication and identifies multiple novel host factors that both restrict and enhance HCMV replication. These studies demonstrate the effectiveness of using systematic approaches for the identification of novel host virus interactions.

L’avortement spontané (AS) désigne la perte du produit de conception avant sa viabilité, c'est-à-dire avant la 22e semaine d’aménorrhée, ou un poids fœtal inférieur à 500 g. La cause génétique est à l’origine de plus des deux tiers des AS, les aneuploïdies autosomiques, représentant à elles seules jusqu’à 70% des pertes fœtales du 1er trimestre. Le caryotype présente une très bonne sensibilité en ce qui concerne le dépistage des trisomies autosomiques (13, 18 et 21) et des aneuploïdies affectant les chromosomes sexuels, mais il montre d’importantes limites, d’une part en raison des échecs de culture cellulaire et d’autre part en raison de l’existence de remaniements non détectables au caryotype standard. Actuellement plusieurs techniques moléculaires de dépistage rapides des aneuploïdies liées aux échecs de grossesses ont été vérifiées : 1°) la fluorescence in situ par hybridation (FISH) 2°) l’amplification multiplex de sondes nucléiques dépendant des ligatures (MLPA). Ces deux méthodes présentent l’avantage d’être réalisables, sans culture préalable, sur noyaux en interphase ou sur ADN extrait et de permettre la détection d’anomalies cryptiques. Notre étude repose sur l’étude cytogénétique des produits d’AS pour mettre en évidence les anomalies chromosomiques les plus fréquentes à l’origine de ces pertes fœtales et d’en mieux appréhender les mécanismes de survenue. Elle a été réalisée sur 220 patientes âgées de 19 à 45 ans, et était fondée sur l’analyse directe par FISH sur noyaux interphasiques (AneuVysionTM) de prélèvements de villosités choriales et sur l’analyse de l’ADN extrait de tissus fœtaux par MLPA afin de révéler d’éventuelles aneuploïdies et micro-remaniements. L’âge gestationnel au moment des prélèvements était compris entre 7 et 38 semaines d’aménorrhée. Sur un total de 151 échantillons analysés par AneuVysionTM, 10 anomalies chromosomiques ont été observées: 3 trisomies 21, 1 trisomie 18, 1 trisomie 13, 1 mosaïque 46,XX/47,XX+21, 3 triploïdies et 1 monosomie X (Turner). Par ailleurs, sur les 69 autres échantillons analysés par MLPA, 6 étaient ininterprétables. Les anomalies trouvées par cette technique étaient: 2 monosomies X. Pour les échantillons restants, la MLPA a été négative. Nous avons en parallèle réalisé une étude rétrospective fondée sur l’analyse comparative d’un échantillon recruté à Sidi Bel Abbès, de femmes ayant subi un AS et admises à la maternité del’hôpital Hassani Abdelkader de Sidi Bel Abbès et d’un échantillon recruté à Clermont-Ferrand de femmes ayant subi un AS et pour lesquelles un prélèvement pour établir le caryotype du produit de fausse-couche avait été adressé dans le service de cytogénétique du CHU Estaing de Clermont-Ferrand. Cette étude a couvert une période de six années, allant de janvier 2005 à décembre 2010. Les techniques de FISH et de MLPA représentent des outils simples, rapides et sensibles pour la détection des remaniements chromosomiques. Elles représentent une alternative très intéressante à la culture cellulaire, et permettent le diagnostic de désordres génomiques indécelables par les techniques conventionnelles. / Spontaneous abortion (SA) is the loss of the product of fertilization before its viability, that is, before22 weeks of gestation or fetal weight less than 500 g. Genetic causes account for more than two thirds of SA, autosomal aneuploidies alone accounting for up to 70% fetal loss. Chromosomal cytogenetic techniques show significant limitations on the one hand because of the failures of cell culture, and secondly because of the existence of undetectable alterations to the standard karyotype. It was therefore planned to use molecular techniques :- Fluorescent in situ hybridization (FISH)- Multiplex ligation-dependent probe amplification (MLPA). Both techniques have the advantage of being achievable without prior culture of cores interphase or DNA extracted and to enable detection of cryptic abnormalities. The project is based on cytogenetic study of AS products to highlight the most frequent chromosomal abnormalities causing fetal losses, and to better understand their occurrence. Our study was performed on 220 patients from 19 to 45 years, and was based on the direct analysis by FISH on interphase nuclei (AneuVysionTM) of chorionic villus sampling and analysis of DNA extracted fetal tissue by MLPA to reveal any aneuploidy and rearrangements. The gestational age of the samples ranged from the 7th to the 38th week of gestation. In a total of 151 samples analyzed by AneuVysionTM, 10 chromosomal abnormalities were observed: three trisomies 21, one trisomy 18, one trisomy 13, one mosaic 46,XX/47,XX+21, 3 triploidies and one monosomy X (Turner). In addition, among the other 69 samples analyzed by MLPA, 6 were uninterpretable. The abnormalities found by this technique were 2 monosomies X. For the remaining samples, the MLPA was negative. We conducted a retrospective parallel study based on the analysis of a sample recruited in Sidi Bel Abbes, women who have had an AS and were admitted to the maternity hospital Abdelkader Hassani, Sidi Bel Abbes ; and a sample recruited in Clermont-Ferrand : women who underwent AS for which a levy to establish the karyotype product miscarriage had been addressed in the Department of Cytogenetics of CHU Estaing, Clermont-Ferrand. This study covered a period of six years, from January 2005 to December 2010. The techniques of FISH and MLPA are simple, rapid and sensitive tools for the detection of chromosomal rearrangements. They represent a very interesting alternative to cell culture and allow diagnosis for genomic disorders undetectable by conventional techniques.

Current single molecule localisation microscopy methods allow for multicolour imaging of macromolecules in cells, and for a degree quantification on molecule numbers in one colour. However, that has not yet been an attempt to develop tools capable of quantitative imaging with multiple colours in cells. This work addressed this challenge by designing linker peptides with chemospecific groups to allow attachment of activator and emitter dyes for STORM imaging, and a targeting module. The design ensured a stoichiometric ratio of targeting module to activator and emitter dyes. Peptides with HaloTag ligands attached were labelled with various activator and emitter pairs and used to label HaloTag fusions of S. pombe and mouse embryonic stem cells. These peptides were found to bind non-specifically to various areas of both cell types, and did not localise to HaloTag protein, whereas controls did. Another peptide was also labelled with activator-emitter pairs and attached to expressed anti-GFP and ant-mCherry nanobodies via native chemical ligation. The labelled anti-GFP nanobody was to demonstrate ensemble and single molecule imaging in S. pombe, as well as characterisation on single molecule surfaces in comparison to a conventional randomly labelled antibody. The stoichiometrically labelled nanobody had a more consistent number of photons detected per localisation, number of localisation per molecule and number of blinks per molecule, which implied that it could be more useful than randomly labelled nanobodies for counting experiments. It was also shown to be capable of specific laser activation for STORM imaging with both an Alexa405Cy5 and Cy3Cy5 pairs. These anti-GFP and anti-mCherry nanobodies and peptide linker are new tools for both counting and multicolour imaging in super-resolution, which could be widely applied to constructs that are already tagged with GFP or mCherry.

<p>A novel technology for protein detection, proximity ligation, has been developed along with improved methods for <i>in situ</i> synthesis of DNA microarrays. Proximity ligation enables a specific and quantitative transformation of proteins present in a sample into nucleic acid sequences. As pairs of so-called proximity probes bind the individual target protein molecules at distinct sites, these reagents are brought in close proximity. The probes consist of a protein specific binding part coupled to an oligonucleotide with either a free 3’- or 5’-end capable of hybridizing to a common connector oligonucleotide. When the probes are in proximity, promoted by target binding, then the DNA strands can be joined by enzymatic ligation. The nucleic acid sequence that is formed can then be amplified and quantitatively detected in a real-time monitored polymerase chain reaction. This convenient assay is simple to perform and allows highly sensitive protein detection. Parallel analysis of multiple proteins by DNA microarray technology is anticipated for proximity ligation and enabled by the information carrying ability of nucleic acids to define the individual proteins. Assays detecting cytokines using SELEX aptamers or antibodies, monoclonal and polyclonal, are presented in the thesis.</p><p>Microarrays synthesized <i>in situ</i> using photolithographic methods generate impure products due to damaged molecules and interrupted synthesis. Through a molecular inversion mechanism presented here, these impurities may be removed. At the end of synthesis, full-length oligonucleotides receive a functional group that can then be made to react with the solid support forming an arched structure. The 3’-ends of the oligonucleotides are then cleaved, removing the impurities from the support and allowing the liberated 3’-hydroxyl to prime polymerase extension reactions from the inverted oligonucleotides. The effect of having pure oligonucleotides probes compared to ones contaminated with shorter variants was investigated in allele specific hybridization reactions. Pure probes were shown to have greater ability to discriminate between matched and singly mismatched targets at optimal hybridization temperatures.</p>

A novel technology for protein detection, proximity ligation, has been developed along with improved methods for in situ synthesis of DNA microarrays. Proximity ligation enables a specific and quantitative transformation of proteins present in a sample into nucleic acid sequences. As pairs of so-called proximity probes bind the individual target protein molecules at distinct sites, these reagents are brought in close proximity. The probes consist of a protein specific binding part coupled to an oligonucleotide with either a free 3’- or 5’-end capable of hybridizing to a common connector oligonucleotide. When the probes are in proximity, promoted by target binding, then the DNA strands can be joined by enzymatic ligation. The nucleic acid sequence that is formed can then be amplified and quantitatively detected in a real-time monitored polymerase chain reaction. This convenient assay is simple to perform and allows highly sensitive protein detection. Parallel analysis of multiple proteins by DNA microarray technology is anticipated for proximity ligation and enabled by the information carrying ability of nucleic acids to define the individual proteins. Assays detecting cytokines using SELEX aptamers or antibodies, monoclonal and polyclonal, are presented in the thesis. Microarrays synthesized in situ using photolithographic methods generate impure products due to damaged molecules and interrupted synthesis. Through a molecular inversion mechanism presented here, these impurities may be removed. At the end of synthesis, full-length oligonucleotides receive a functional group that can then be made to react with the solid support forming an arched structure. The 3’-ends of the oligonucleotides are then cleaved, removing the impurities from the support and allowing the liberated 3’-hydroxyl to prime polymerase extension reactions from the inverted oligonucleotides. The effect of having pure oligonucleotides probes compared to ones contaminated with shorter variants was investigated in allele specific hybridization reactions. Pure probes were shown to have greater ability to discriminate between matched and singly mismatched targets at optimal hybridization temperatures.

Novel techniques are needed to investigate the genetic variation revealed in the first draft of the human genome sequence. Padlock probes are recently developed reagents, suitable for detecting single-nucleotide variations of DNA and RNA in situ or in solution. The probes are oligonucleotides of about 70-140 nucleotides that can be circularized by ligation in the presence of a correct target sequence. Standard chemical synthesis of padlock probes is difficult due to the requirement for intact 5' and 3' ends of these long oligonucleotides. A novel PCR-based method is presented in this thesis, whereby longer, densely labeled padlock probes can be made as compared to conventional chemical synthesis. PCR-generated padlock probes produced a stronger signal and a more resolved staining pattern, compared to chemically synthesized probes in fluorescence in situ analysis of an alpha-satellite sequence variant present in human chromosomes 13 and 21. Padlock probes used for in situ analysis of metaphase chromosomes had an optimal length of 140 nucleotides. They were used to identify individual chromosomes 7 and 15, and to follow the transmission of chromosome homologues for two consecutive generations. The specificity of the padlock probes to detect single copy genes in genomic DNA samples was demonstrated by detecting a single-nucleotide mutation in the ATP7B gene. It has not previously been known if T4 DNA ligase can be used for RNA sequence analysis. In this thesis, it is demonstrated that T4 DNA ligase can be used for distinguishing single-nucleotide RNA sequence variants. Reaction conditions were defined where most mismatches could be discriminated by a factor of 80 and all mismatches by a factor of at least 20. Under these conditions padlock probes could detect and distinguish RNA sequence variants with ligation efficiency almost as high as on the corresponding DNA sequence. A detailed study of the parameters influencing RNA-templated DNA ligation revealed that DNA ligation on RNA templates proceeds at a much slower rate compared to the same reaction on DNA, and that a molar excess of enzyme is required. Furthermore, the ligation reaction is inhibited by high concentrations of the cofactor ATP and NaCl. The work presented in this thesis demonstrates that PCR-generated padlock probes can detect and distinguish single-nucleotide variation in both RNA and DNA.