<p>Cytochrome c (Cyt c) is a heme-containing protein that is a component of the electron transport chain as well as the mitochondrial apoptotic pathway. It is released from the mitochondrial intermembrane space to the cytosol during apoptosis and is also thought to be a biomarker for cancer and liver disease. Therefore, an efficient Cyt c biosensor would be a very useful tool for studying apoptosis. Here we show the process of development of Cyt c-dependent aptazymes, derived by <em>in vitro </em>selection. These aptazymes consist of 3 components: 1) a substrate with a cleavage site that consists of a single ribonucleotide flanked by a fluorophore and quencher; 2) a DNAzyme (catalytic DNA) motif capable of cleaving the substrate; 3) an aptamer, a short piece of single- stranded DNA that can specifically bind Cyt c. When Cyt c is absent, the aptamer occludes the catalytic core of the DNAzyme and the fluorophore of the intact substrate is quenched. However, when Cyt c is present, the aptamer binds Cyt c, allowing the DNAzyme to cleave the embedded ribonucleotide, separating the fluorophore and quencher, resulting in a fluorescent signal. Simulations of <em>in vitro </em>selection of Cyt c- dependent aptazymes were also performed. The simulations revealed several methods that can improve the success rate of future <em>in vitro </em>selections of aptazymes.</p> <p>Further analysis of the previously derived DNAzyme DEC22-18 was also performed. A detailed understanding of this DNAzyme will allow it to be developed into a biosensor.</p> / Master of Science (MSc)

The RNA World Hypothesis posits that RNA enzymes (ribozymes) catalyzed biochemical reactions in primitive cells prior to the emergence of proteins. However, the evolutionary mechanisms that gave rise to functional RNA sequences on early Earth remains largely unclear. Using a bottom-up approach that combines in vitro selection and high-throughput sequencing, we demonstrate how a self-cleaving RNA enzyme, the Hammerhead Ribozyme (HHR), may have evolved from non-catalytic sequences in the RNA World. Multiple starting libraries were generated by progressively increasing the number of randomized positions in the ribozyme’s catalytic core. The HHR was selected from each of these libraries following several rounds of amplification and enrichment. Deep sequencing analysis was then used to track evolutionary trends that gave rise to the wild-type sequence during each selection. This novel approach revealed a wide range of functional HHR variants. Notably, we discovered active hammerhead variants with mutations to previously identified essential nucleotides, shedding new light on the sequence requirements of the full-length, cis-acting ribozyme. We also demonstrate that the evolutionary trajectory of each nucleotide in the catalytic core directly correlates with their functional importance, potentially giving researchers a novel method to assess the sequence requirements of functional nucleic acids. Altogether, the in vitro evolution of ribozymes shows how complex molecules might have emerged from non-catalytic polymers in the RNA world, contributing to our understanding of the origin of life on Earth. / Thesis / Master of Science (MSc) / The origin of life is complicated by the interdependence between deoxyribonucleic acid (DNA), which stores genetic information, and protein, which performs essential cellular functions. The RNA World Hypothesis attempts to solve this paradox by underpinning ribonucleic acid (RNA) as the foundation of cellular based-life, due to its unique ability to store genetic information as well as perform complex chemical reactions. However, the way that functional RNA molecules (ribozymes) emerged on early Earth in the first place remains largely unclear. We simulated molecular evolution in the laboratory using a process known as in vitro selection to demonstrate how a self-cleaving RNA enzyme, the Hammerhead Ribozyme (HHR), may have evolved in the RNA World. We also discovered different versions of the HHR, shedding new light on its structure and function. Altogether, the results from this work pave the way for a deeper understanding of ribozyme evolution and the origins of life on Earth.

Orientador: Selma Giorgio / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T13:17:36Z (GMT). No. of bitstreams: 1 Costa_SolangedosSantos_M.pdf: 4660323 bytes, checksum: 5aef15cb049a82091dd076c48c1f6f2b (MD5) Previous issue date: 2010 / Mestrado / Parasitologia / Mestre em Parasitologia

Les ARN non-codants exercent des rôles essentiels au sein de nombreux processus biologiques, allant de la régulation de l’expression génique à l’activité enzymatique. Afin de remplir leurs fonctions cellulaires, ces ARN doivent adopter des structures tridimensionnelles spécifiques, et mieux comprendre ces structures et leur dynamique est crucial pour élucider leur mécanisme d’action et créer des ARN possédant de nouvelles fonctions. Afin de mieux comprendre la structure, la dynamique et l’ingénierie des ARN, notre laboratoire étudie le ribozyme VS de Neurospora, un petit ARN (~160 nucléotides) possédant une activité catalytique. Le ribozyme VS a été découvert il y a une trentaine d’années chez certains isolats naturels du champignon microscopique Neurospora. Ce ribozyme a fait l’objet d’études approfondies et est considéré comme étant un système modèle idéal pour étudier la structure et la fonction de l’ARN in vitro, en raison de sa taille relativement petite, de sa structure tridimensionnelle complexe et de son activité enzymatique facilement détectable. Comme plusieurs autres ribozymes de sa famille, le ribozyme VS catalyse des réactions de clivage et de ligation d’une liaison phosphodiester spécifique. Toutefois, il a la capacité unique de reconnaître et de cliver un substrat isolé, replié sous forme de tige-boucle, par l’entremise d’une interaction boucle-boucle extrêmement stable, une caractéristique intéressante d’un point de vue de l’ingénierie de l’ARN. Des structures cristallines récentes ont fourni de l’information importante à propos de l’état fermé du ribozyme, qui comprend un site actif pré-catalytique. Toutefois, des études récentes ont plutôt démontré que le ribozyme VS adopte un état ouvert en solution et il n’existe que très peu d’information structurale sur cet état et sur les mécanismes de transition menant à la forme fermée. Afin de caractériser la structure du ribozyme en solution, une stratégie modulaire de divide-and-conquer a été entreprise et des structures RMN à haute résolution de chacun des sous-domaines structuraux clés ont été déterminées. Cette thèse vise à caractériser la structure du ribozyme VS complet en solution et à explorer sa capacité à cliver une molécule d’intérêt différente de son substrat naturel. Dans un premier temps, une étude d’ingénierie a été entreprise afin de créer des variants du ribozyme VS capables de reconnaître une tige-boucle d’ARN dérivée de l’Élément de Réponse de Transactivation du virus d’immunodéficience humaine (VIH). Ainsi, des variants hautement actifs du ribozyme ont été identifiés par sélection in vitro et une étude complémentaire de dynamique moléculaire a démontré que l’interaction boucle-boucle agit à titre de charnière dynamique et facilite la formation de l’état fermé du ribozyme. L’approche structurale de divide-and-conquer a ensuite été complétée en combinant des études de RMN et de diffusion des rayons-X aux petits angles (SAXS). Ainsi, des structures à haute résolution du domaine catalytique minimal et d’un complexe formé entre un ribozyme VS plus étendu et un substrat non-clivable ont alors été obtenus. En comparant ces structures aux structures cristallines, nous avons découvert un réarrangement structural important associé à la formation du site actif. Dans l’ensemble, ces travaux offrent une meilleure compréhension de l’architecture globale du ribozyme VS et de son mécanisme d’action qui comprend un échange dynamique de multiples états conformationnels. Plus généralement, les leçons apprises ici permettront de mieux guider les expériences d’ingénierie du ribozyme VS et d’autres ARN fonctionnels. / Non-coding RNAs play essential roles in many biological processes, ranging from the regulation of gene expression to enzymatic activity. To perform their cellular functions, RNAs must adopt specific three-dimensional structures, and understanding how these structures fold is crucial to elucidate their mechanism of action. However, our fundamental understanding of the structure and dynamics of RNA at atomic resolution remains rather limited. To better understand the structure, dynamics and engineering of RNA, our laboratory is investigating the Neurospora VS ribozyme, a small RNA (~160 nucleotides) with catalytic activity. The VS ribozyme was originally found 30 years ago in natural isolates of Neurospora fungi. It has been thoroughly investigated as an ideal model system to study the structure and function of RNA in vitro, due to its small size, its complex three-dimensional structure and easily detectable activity. Like other small nucleolytic ribozymes, the VS ribozyme catalyzes the cleavage and ligation reactions of a specific phosphodiester bond. However, it has the unique ability to recognize and cleave an isolated hairpin substrate through the formation of a highly stable kissing-loop interaction, which is of great interest for RNA engineering purposes. Recent crystal structures have provided useful information on the closed state of the ribozyme, in which the active site is formed. However, the VS ribozyme is also known to adopt an open state in solution and there is still very little structural information regarding this state and how it is converted into the active closed state. In order to characterize the solution structure of the ribozyme and its dynamics, an NMR-based divide-and-conquer approach was previously undertaken in which high-resolution structures of each of the key structural subdomains were determined. The work presented in this thesis aims to characterize the structure of the complete VS ribozyme in solution and to explore its ability to cleave an RNA hairpin of interest, different from its natural substrate. First, an engineering study was undertaken to create VS ribozyme variants capable of recognizing an RNA stem-loop derived from the HIV-1 Trans-Activation Response Element RNA. Using in vitro selection, highly active ribozyme variants were identified, and their sequence analysis suggests that the improved activity observed in some variants depends on increased conformational sampling of the kissing-loop interaction. Complementary molecular dynamics studies indicate that the kissing-loop interaction acts as a dynamic hinge to facilitate the formation of the closed state of the ribozyme. Next, the divide-and-conquer approach for structural investigation of the VS ribozyme was completed by combining NMR and small-angle X-ray scattering (SAXS) data. High-resolution structures were determined for both a minimal catalytic domain and a complex between a more extended trans ribozyme and a non-cleavable substrate. By comparing these solution structures to the previously reported crystal structures, we uncovered an important structural rearrangement associated with the formation of the active site. Overall, this work provides a better understanding of the global architecture of the VS ribozyme and how it fulfills its function by dynamic exchange of many conformational states. More generally, the structural and dynamic knowledge generated from this work will help to guide future engineering studies of the VS ribozyme and other functional RNAs.

This project is aimed toward finding DNA aptamers against prostate cancer peptide antigens. DNA aptamers can function to find and indicate the presence of certain molecules in a specimen. These aptamers will be obtained through the process of evolutionary selection, a specific process called SELEX which stands for Systemic Evolution of Ligands by Experimental Enrichment. By conducting several rounds of SELEX, a DNA aptamer will be selected to bind to a known peptide antigen. A biotinylated column will be utilized to stabilize a random library of DNA aptamers, and those peptides that bind to certain aptamers will cause a conformational change leading to the elution of those specific DNA aptamers. This SELEX process will be conducted again on the eluted aptamers to further select for strong binding DNA aptamers. The DNA aptamers that are obtained can further on be sequenced or used for prostate cancer research studies. Another possible usage of aptamers is to diagnose and determine the stage of various different cancer types. Our prediction is that this research will produce a DNA aptamer that will bind to a specific prostate cancer peptide antigen.

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