Dissertations / Theses: 'DNA Substrates'

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Riley, Jane. "The interaction of topoisomerase IV with potential DNA substrates." Thesis, University of Liverpool, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272768.

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Gössl, Illdiko Maria. "Supramolecular structures of dendronized polymers and DNA on solid substrates." [S.l.] : [s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968755925.

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Bergen, Konrad [Verfasser]. "Structural insights into DNA polymerases encountering aberrant substrates / Konrad Bergen." Konstanz : Bibliothek der Universität Konstanz, 2015. http://d-nb.info/1078230455/34.

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Gössl, Illdiko Maria. "Supramolecular structures of dendronized polymers and DNA on solid substrates." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2003. http://dx.doi.org/10.18452/14893.

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Komplexe aus entgegengesetzt geladenen Polyelektrolyten haben sowohl in der Biologie als auch in den Materialwissenschaften eine große Bedeutung. Im Mittelpunkt des Interesses stehen besonders die Kondensation der DNA in vitro, die Struktur des Nukleosoms im Zellkern, nicht-virale Systeme zur Transfektion von DNA in Zellen oder der Vorgang der layer-by-layer Adsorption. Verschiedene Theorien befassen sich mit den treibenden Kräften solcher Komplexbildungen. Allerdings standen experimentelle Untersuchungen auf diesem Gebiet bisher noch aus. Dieser Arbeit liegt die Fragestellung zu Grunde, ob es mit Hilfe der Rasterkraftmikroskopie möglich ist, die Struktur einzelner Polyelektrolytkomplexe, bestehend aus den beiden Polyelektrolyten DNA und dendronisierten Polymer, aufzuklären und ihre Komplexbildung zu untersuchen. Die Komplexe bildeten sich in Lösung und wurden anschließend auf einer unbeschichteten oder mit positiven Polymeren beschichteten Glimmeroberfläche adsorbiert. Auf der positiv beschichteten Glimmeroberfläche hafteten DNA-dendronisierte Polymer Komplexe mit einem Ladungsverhältnis von 1:1 bis 1:0.7 (DNA:dendronisiertes Polymer). Anhand der hochaufgelösten rasterkraftmikroskopischen Aufnahmen wurde ein Modell entwickelt, das die Umwicklung der DNA um das dendronisierte Polymer beschreibt. Der DNA-DNA Abstand ergab sich zu (2.30 ± 0.27) nm für den Komplex mit DNA und zweiter Generation dendronisierter Polymere und zu (2.16 ± 0.27) nm mit vierter Generation. Die theoretische Vorhersage der Überladung der Komplexe konnte experimentell bestätigt werden. Mit Hilfe der Rasterkraftmikroskopie konnte überdies der Einfluss des Salzgehaltes der Lösung auf die Bildung der Komplexe mit DNA und zweiter Generation dendronisierter Polymere untersucht werden. Wie man anhand des Zusammenwirkens von elektrostatischen Kräften und entropischen Wechselwirkungen bei der Adsorption von Polyelektrolyten vorhersagen kann, durchlief der DNA-DNA Abstand ein Minimum bei ansteigendem Salzgehalt. Bei sehr hohem Salzgehalt (2.4 M NaCl) konnte das Ablösen der DNA von dem Komplex beobachtet werden. Die untersuchten DNA/dendroniserten Polymer Komplexe bilden ein neues Modellsystem, mit dem einzelne Polyelektrolyt-Wechselwirkungen direkt untersucht werden können. Ein Vergleich der experimentellen Daten mit den vorhandenen Theorien zeigte, dass der Prozess des Überladens weitgehend durch elektrostatische Wechselwirkung zwischen den beiden Polyelektrolyten beschrieben werden kann. Sowohl entropische Beiträge als auch die Biegeenergie der umwickelnden DNA sind vernachlässigbar. Basierend auf diesen Ergebnissen können neue Trägerstrukturen für effizientere nicht-virale DNA-Transfektionssysteme entwickelt werden. Complexes of oppositely charged polyelectrolytes play an important role in both biology and material science, for instance DNA condensation in vitro, nucleosomal structure, non-viral gene transfection systems as well as layer-by-layer adsorption. Although there are theories predicting overcharging of polyelectrolyte complexes, the driving forces are still under debate and systematic experimental studies on single polyelectrolytes remain challenging. Therefore the question arose if it is possible to analyze single polyelectrolyte complexes, using DNA and dendronized polymers, with the scanning force microscope in order to investigate the complexation in detail. For the complex analysis, the polyelectrolytes were allowed to interact in solution and then to adsorb on negatively charged mica or on mica coated with a positively charged polymer. Scanning force microscopy was used to investigate the adsorbed species. DNA/dendronized polymer complexes of charge ratio of 1/1 through 1/0.7 adsorbed on mica coated with a positively charged polymer. The analysis of high resolution molecular images indicated that DNA wraps around the dendronized polymer with an estimated pitch of (2.30 ± 0.27) nm and (2.16 ± 0.27) nm for dendronized polymers of generation two and four, respectively. In the proposed model the polyelectrolyte with the smaller linear charge density is wrapped around the more highly charged dendronized polymer, resulting in a negatively overcharged complex. This overcharging is consistent within recent theories of spontaneous overcharging of complexes of one polyelectrolyte wrapping around the other. Using the complex of DNA and dendronized polymers of second generation, the influence of monovalent salt concentration on the molecular structure was studied. By increasing the salt concentration the pitch showed a minimum as predicted by the interplay of electrostatic forces and entropic interactions of polyelectrolyte adsorption. At high salt concentration (2.4 M NaCl) the release of DNA from the complex can be observed. The results showed that the DNA/dendronized polymer system can be used as a new, high potential model system to investigate single polyelectrolyte interactions. With regard to recent theories, the experimental results indicate that the overcharging of the complex is mainly driven by electrostatic forces whereas contributions of counterion entropy and bending energy seem to be negligible. This understanding may be useful for the design of single polyelectrolyte complexes for non-viral gene delivery systems and might help to optimize the transfection efficiency based on the structure of the vector system.

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Blatter, Nina [Verfasser]. "DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase: A Functional and Structural Analysis / Nina Blatter." Konstanz : Bibliothek der Universität Konstanz, 2013. http://d-nb.info/105832599X/34.

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Ren, Ruobo. "DNA printing on polymer substrates : towards cost-effective medical diagnostic devices." Thesis, Swansea University, 2011. https://cronfa.swan.ac.uk/Record/cronfa43015.

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DNA for sensing has a diversity o f life science applications. The aim o f this work was to explore the printing DNA onto a flexible substrate. DNA printing has a diversity of life science applications. DNA can be printed onto rigid substrates at high resolution. Printing is a candidate process for volume manufacturing. This required identification o f substrate and any surface treatment to ensure wetting and adhesion. Printing also involves matching the ink with printing process characteristics and for the purpose o f sensing, it requires the formulation o f an ink that can be printed and demonstrates suitable hybridisation characteristics. Each of these aspects was addressed within this thesis. Measurement techniques and their robustness were established as a first step. The next stage focused on determining a suitable substrate and surface treatment for immobilisation o f DNA. This was followed by an exploration o f printing processes, which include inkjet as a reference and flexography and gravure as candidates for volume printing. This work was carried out on a bench top printed, while providing a path for volume printing. The third research strand was concerned with the hybridisation of DNA formulated within an ink. A CCP (Corona treated top coated BOPP) substrate was found to enable good immobilisation o f DNA It needed to be corona treated to enhance the covalent bonding mechanism. Inkjet printing was successfully in applying out, however, within the range o f process parameters explored, neither flexography nor gravure successfully printed DNA. Further work is needed to develop them so they successfully print and could be used for volume production. An appropriate hybridisation method for DNA deposited within an ink formulation was established.

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Roewenstrunk, Julia Maria 1981. "RNF169 and RNF168 novel substrates of DYRK1A : connecting DYRK1A to DNA-damage repair." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/565442.

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Gene dosage alterations of the kinase DYRK1A are linked to disease in humans. To better understand DYRK1A activities an interactome analysis was performed. RNF169, an E3-ubiquitin ligase key component of the cellular response to double-strand breaks (DSBs), was found as a top nuclear interactor. The functional characterization of this interaction has uncovered that a dedicated motif in the non-catalytic N-terminus of DYRK1A is responsible of the direct interaction with RNF169 and that this interaction is essential for the recruitment of DYRK1A to DSBs. Using a combination of mass spectrometry analysis, mutagenesis, and in vitro kinase assays several DYRK1A-dependent phosphosites have been identified in RNF169 and its paralog RNF168. Reporter-cell assays and IRIF analysis showed that DYRK1A silencing perturbs the DSB-repair pathways. In agreement, DYRK1A knockdown leads to increased radiation sensitivity. All together, the data suggest a role for DYRK1A in DSB-repair that might involve the phosphorylation of RNF168 and RNF169. Alteraciones de la dosis génica de la quinasa DYRK1A son causantes de enfermedad en humanos. Para profundizar en las actividades biológicas de DYRK1A, se ha realizado un estudio de interactoma, en el que RNF169, elemento clave en la respuesta al daño al DNA causado por roturas de doble cadena, se reveló como uno de los principales interactores. La interacción DYRK1A-RNF169 es directa y responsable de la localización de DYRK1A en el DNA en respuesta al daño. La combinación de espectrometría de masas, mutagénesis y ensayos quinasa ha permitido identificar varios residuos fosforilados por DYRK1A en RNF169 y en su parálogo RNF168, que actúa en el mismo proceso. El silenciamiento de DYRK1A causa alteraciones en los mecanismos de respuesta al daño y las células presentan un aumento de la sensibilidad a la radiación. Estos resultados permiten sugerir que DYRK1A puede ser un nuevo regulador de la respuesta al daño al DNA.

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Baker, Bryan Alexander. "Employing double-stranded DNA probes on colloidal substrates for competitive hybridization events." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/33922.

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The study of the DNA has found application beyond our understanding of its cellular function and into a variety of materials assembly and nucleic acid detection systems. The current research investigates double-stranded DNA probes in both a colloidal particle assembly and fluorescent assay format utilizing competitive hybridization events. In both contexts, the affinity of the dsProbes is tuned by the sequence design parameters of duplex length and complementarity. These systems were incubated with nucleic acid targets of interest and, based on the mechanism of competitive hybridization, were responsive to the presence of a high affinity competitive target. In the case of the particle assemblies, incubation with the competitive target resulted in observable disassembly of particle structures. In the case of fluorescently labeled dsProbes, incubation with competitive targets resulted in a quantifiable loss of fluorescence as determined by flow cytometry. Utilizing the fluorescently labeled dsProbe system, the kinetics of competitive hybridization was characterized for nucleic acid targets of varying specificity and strand context. The results indicate promise for the development of the competitive hybridization approach in nucleic acid detection systems providing advantages over current single-stranded probe designs. By utilizing a fluorescently labeled dsProbe approach, it is unnecessary to chemically modify the target of interest to impart a signaling mechanism. Additionally, as the process of competitive hybridization of dsProbes with targets of interest is an affinity driven process, discrimination of targets based on specificity is decoupled from standard measures such as elevated temperature protocols, an important step in translating nucleic acid technologies from the controlled laboratory environment to field applications.

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Tapp, Maeling Janelle Nicole. "Competition-induced selection of ligands for the screening of DNA aptamers for gold substrates." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54851.

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This dissertation presents the development of an alternative aptamer screening process, Competition-Induced Selection of Ligands (CISL), and its use in screening for ssDNA aptamers for gold substrates. Gold substrates are presented as the nonnucleotide target for implementing CISL as a novel aptamer screening approach. Chapter 1 provides an overview of the in vitro selection of oligonucleotide aptamers, the polymerase chain reaction that is a key step in the aptamer screening process, the synthesis and properties of gold nanoparticles and the biomolecule-mediated formation of inorganic nanoparticles. Chapter 2 presents the goals and objectives of this thesis along with an organizational overview of the dissertation. Chapter 3 describes the experimental techniques and optimizations pertinent to the development of the CISL aptamer screening process. Chapter 4 investigates the effects of various nucleic acid additions during the seed-mediated growth of gold nanoparticles. Chapter 5 discusses the use of CISL in screening for ssDNA aptamer candidates for spherical gold nanoparticles (AuNPs) and the primary and secondary structure analysis of identified sequences. Chapter 6 presents the use of CISL in screening for ssDNA aptamer candidates for planar gold substrates (PlanarAu) and also includes primary and secondary structure analysis of identified sequences accompanied with an incubation study to provide a “frequency” ranking of aptamers as adsorbate species on PlanarAu. Chapter 7 offers concluding remarks and ideas for future expansion and applications of this work.

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Grealy, Alicia Catherine. "New approaches to ancient DNA: using novel substrates to characterise DNA preservation and past biodiversity in warm-climate ecosystems." Thesis, Curtin University, 2016. http://hdl.handle.net/20.500.11937/51741.

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Retrieving ancient DNA (aDNA) from fossils in warm, tropical environments remains a challenge. This thesis describes the development and application of next generation sequencing technologies in the search for warm-climate aDNA. Methods to extract, enrich and sequence aDNA from fossil ‘bulk bone’ and avian eggshell are successfully explored from sites in Australia and Madagascar. Collectively, the research provides new insights into past biodiversity and evolutionary processes in climates not previously considered conducive to DNA preservation.

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Johnson, Christopher N. "Nucleic Acid Substrates: Investigation of Structural and Dynamic Features that Influence Enzyme Activity." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/chemistry_diss/59.

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The previous view of DNA as a linear sequence of bases is evolving to consider structure, topology and dynamics. Sequences surrounding damage lesions have been shown to effect enzyme recognition and processing. Here we present an in depth investigation of subtle structural and dynamical features imparted to nucleic acid duplexes by a designed modification or damage lesions. Highly restrained solution structures were generated and validated utilizing a range of NMR techniques. This allowed for the characterization of multiple features of the nucleic acid duplex; such as base pairing, backbone torsion angles, deoxyribose sugar pucker, and intra and inter nucleotide proton distances. Additional experiments provided insight into dynamic movements of the nucleic bases. These features are then correlated to enzyme data in order to explain the observed modulation of activity.

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Malytska, Iuliia. "Exploring bipolar electrochemistry for the modification of unusual conducting substrates." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0135/document.

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L'électrochimie bipolaire est un phénomène basé sur la polarisation d'un objet conducteur soumis à un champ électrique. Contrairement à l'électrochimie conventionnelle, c’est la chute de potentiel en solution imposée par les deux électrodes sources qui permet de réaliser les réactions électrochimiques. Lorsqu'un objet conducteur est immergé dans une solution électrolytique et soumis à un champ électrique, il est polarisé et se comporte comme une électrode bipolaire. La différence de potentiel entre l'électrolyte et l'électrode bipolaire est la force motrice pour les réactions de réduction et d’oxydation promus aux deux extrémités de l'électrode bipolaire. L'oxydation se produira à l’une des extrémités, combinée simultanément avec la réduction à l'autre extrémité.L'électrochimie bipolaire est une technique d’adressage sans fil qui permet de générer une réactivité électrochimique asymétrique à la surface d'un objet conducteur. Au cours de la dernière décennie, l'électrochimie bipolaire a trouvé de nombreuses applications telles que la synthèse de micro- et nanoparticules asymétriques, l'électrodéposition, la détection, la propulsion de micro-objets, etc. L'avantage de cette technique repose sur le mode d’adressage sans fil qui peut être utilisé pour modifier des matériaux fragiles sans contact ou encore pour modifier simultanément un ensemble de particules en même temps.Dans la présente thèse, l'électrochimie bipolaire a été appliquée à différents matériaux semi-conducteurs et systèmes biologiques. De plus, les nouvelles propriétés générées sur ces nouveaux substrats ont été étudiées en utilisant diverses techniques de caractérisation.L'électrodéposition bipolaire est un outil de choix pour la génération d'objets asymétriques. En utilisant cette approche, un dépôt de métal a été réalisé sur substrats organiques de type complexes de transfert de charge. Ces nouveaux matériaux hybrides métal/organique se sont révélés de bons candidats pour la génération asymétrique de photo-voltage sous illumination.Un matériau semi-conducteur inorganique, tel que les dichalcogénures de métaux de transition a également été utilisé comme substrat pour l'électrochimie bipolaire. Différents dépôts de métaux ont été réalisés sur les macro-particules de MoSe2. Les dichalcogénures de métaux de transition sont également connus pour leur activité électrocatalytique, notamment pour la réaction d'évolution de l'hydrogène. La production d'hydrogène sans fil sur des cristaux de MoSe2 a également été réalisée par électrochimie bipolaire. De plus, l'électrochimie bipolaire peut être utilisée avec une suspension de microparticules de MoSe2 pour réaliser une électrolyse quantitative d’une solution contenant une espèce chimique oxydable.Enfin, l'électrochimie bipolaire pourrait également être utilisée pour étudier indirectement la conductivité de molécules biologiques telles que l’ADN. L'objectif principal était de développer une méthode en électrochimie bipolaire pour la modification asymétrique de l'ADN par des nanoparticules métalliques. Tout d'abord, des expériences ont été réalisées en utilisant l'électrodéposition bipolaire à l’aide d’une électrophorèse capillaire (CABED) suivie d'une imagerie par TEM. Des résultats positifs ont été obtenus mais avec une faible reproductibilité.La seconde approche consiste à étirer des molécules d'ADN sur une surface isolante par peignage et à visualiser cette fois-ci les dépôts par microcopie AFM Bipolar electrochemistry is a phenomenon based on the polarization of conductive objects in an electric field. In contrast to conventional electrochemistry, the drop of potential in the electrolyte solution triggers the involved redox reactions. When a conductive object is positioned in an electric field present in a solution between two feeder electrodes, it is polarized and becomes a bipolar electrode. The potential difference between the electrolyte and the bipolar electrode is the driving force for reduction/oxidation reactions at the two extremities of the bipolar electrode; oxidation will occur at one end, combined simultaneously with reduction at the other end.Bipolar electrochemistry is a concept that allows generating an asymmetric reactivity at the surface of a conductive object. During the last decade, bipolar electrochemistry found many applications such as the synthesis of asymmetric micro- and nano-particles, electrodeposition, sensing, propulsion of microobjects, electroanalysis etc. The advantage of this technique is its wireless character, which allows the modification of delicate materials and also to electrochemically address many objects simultaneously.In the present thesis, the approach was applied to different semiconducting materials and biological systems. In addition, properties of substrates of different nature have been studied using bipolar electrochemistry.In this way, it was possible to create metal deposits on organic charge transfer salts in a site-specific way. The resulting hybrid metal/organic particles were tested for the asymmetric generation of photovoltage under illumination.Inorganic transition metal dichalcogenides were also used as a substrate for bipolar electrochemistry. Deposition of different metals on MoSe2 macroparticles was performed. Transition metal dichalcogenides are known for their catalytic activity with respect to hydrogen evolution reaction. Therefore, wireless hydrogen production on MoSe2 crystals and microparticles could be demonstrated by using bipolar electrochemistry. In the latter case it is possible to envision their use for electrochemical decontamination of solutions in the bulk.Finally, bipolar electrochemistry has also been used for studying the conductivity of biological molecules (DNA). The primary goal was to develop a new approach for the asymmetric modification of DNA by metal nanoparticles. Experiments were performed by using either Capillary Assisted Bipolar Electrodeposition (CABED) with the DNA molecules present in the bulk, or by immobilizing DNA as stretched entities on model surfaces for subsequent modification. Encouraging first results could be evidenced by TEM or AFM measurements

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Smith, Paul Andrew. "Simulation studies of alkanes and surfactants." Thesis, Queen's University Belfast, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314225.

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Obeid, Samra [Verfasser]. "Snapshots of DNA polymerase processing aberrant substrates : Structural insights into abasic site bypass and polymerization of 5-alkynylated nucleotide analogs / Samra Obeid." Konstanz : Bibliothek der Universität Konstanz, 2011. http://d-nb.info/1024457699/34.

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Sy, Piecco Kurt Waldo. "Chemically-Patterned Substrates via Sequential Photoinitiated Thiol-ene Reactions asTemplates for the Deposition of Molecules and Materials on Surfaces." Ohio University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1553174280949411.

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Prinz, Julia [Verfasser], Ilko [Akademischer Betreuer] Bald, Tim [Gutachter] Liedl, and Michael Uwe [Gutachter] Kumke. "DNA origami substrates as a versatile tool for surface-enhanced Raman scattering (SERS) / Julia Prinz ; Gutachter: Tim Liedl, Michael Uwe Kumke ; Betreuer: Ilko Bald." Potsdam : Universität Potsdam, 2017. http://d-nb.info/1218793171/34.

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Cary, ReJeana. "Sensing of Small Molecules, Biomarkers, and Pathogens using Unique Plasmonic Assay Platforms." University of Cincinnati / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1595848703283784.

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Ahn, Jinwoo. "DNA polymerase ? : Control of substrate specificity and fidelity /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487943610785207.

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Björnberg, Olof. "Viral dUTPases recombinant expression, purification, and substrate specificity /." [Lund] : Dept. of Biochemistry, Lund University, Sweden, 1995. http://books.google.com/books?id=hvZqAAAAMAAJ.

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Cohen, H. "Investigating and engineering the substrate specificity of DNA methyltransferases." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597811.

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DNA methyltransferases catalyse the transfer of methyl groups from the cofactor S-adenosyl-L-methionine to a target base (adenine or cytosine) within a cognate recognition sequence. I have studied cofactor binding, DNA specificity and the role of conserved amino acid motifs in the cytosine C5 methyltransferase M.HaeIII. By measuring the competitive inhibition of methylation by a series of cofactor analogues, each modified at a single position, the importance of each functional group for cofactor binding to M.HaeIII was probed. The functional significance of amino-acid residues in M.HaeIII was investigated using in vitro compartmentalisation (IVC), an activity-based selection method. IVC was used to obtain active variants of M.HaeIII from libraries diversified at conserved motifs in the catalytic and DNA binding domains. M.HaeIII modifies the central cytosine of the sequence (5’-GGCC-3’). Using bisulphite sequencing, cytosines in a variety of other sequence contexts were found to be methylated at lower levels by M.HaeIII both in vivo and in vitro. IVC was then used to select mutant enzymes with an improved ability to methylate the non-canonical site AGCC.

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Ong, Jennifer Lee. "Directed evolution of DNA polymerases with altered substrate specificities." Thesis, University of Cambridge, 2004. https://www.repository.cam.ac.uk/handle/1810/284037.

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Huber, Michael D. "Structure-function analysis and substrate specific inhibition of RecQ helicases /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9253.

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Matta, Elie. "Characterization of DNA ADP-Ribosylation Mechanism and its Role in DNA Damage Signaling Insight into DNA Substrate Specificity of PARP1-Catalysed DNA Poly(ADP-Ribosyl)ation Role of PARP-catalyzed ADP-ribosylation in the Crosstalk Between DNA Strand Breaks and Epigenetic Regulation." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS058.

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Les poly (ADP-ribose) polymérases dépendantes de l’ADN (PARPs) PARP1, PARP2 et PARP3 agissent comme des détecteurs de cassures d'ADN signalant des dommages à l'ADN. Lors de la détection des dommages à l'ADN, ces PARPs utilisent le nicotinamide adénine dinucléotide comme substrat pour synthétiser un monomère ou un polymère d'ADP-ribose (MAR ou PAR, respectivement) attaché de manière covalente au résidu accepteur des protéines cibles. Récemment, il a été démontré que les protéines PARP1–3 peuvent directement ADP-ribosyler les cassures d'ADN en attachant les oligomères MAR et PAR aux phosphates terminaux.Néanmoins, peu de choses sont connues sur les mécanismes régissant la reconnaissance et la spécificité du substrat de PARP1, qui représente la majeure partie de l'activité de PARylation cellulaire, ainsi que sur les protéines responsables de la détection et de l'élimination des adduits d'ADN ADP-ribosylés et son rôle dans une multitude de processus cellulaires. Dans cette étude, nous avons caractérisé de manière détaillée la spécificité du substrat (ADN) de PARP1 et des mécanismes de la PARylation de l'ADN. Nous avons montré que le résidu phosphate 3'-terminal aux extrémités des cassures de l'ADN double brin servait de site accepteur majeur pour la PARylation catalysée par PARP1 en fonction de l'orientation et de la distance entre les cassures du brin d'ADN dans une seule molécule d'ADN. De plus, une préférence pour l’ADP-ribosylation des molécules d'ADN contenant du phosphate 3'-terminal a été observée par rapport à l'auto-ADP-ribosylation de PARP1, et un modèle de modification de l'ADN par PARP1 a été proposé. Des résultats similaires ont été observés avec l’enzyme PARP1 recombinante purifiée et des extraits provenant des cellules HeLa. Ainsi, les effets biologiques de l’ADP-ribosylation médiée par PARP peuvent dépendre fortement de la configuration des cassures complexes des brins d'ADN. De plus, nous avons élaboré une nouvelle approche permettant d’identifier et valider les protéines responsables de la détection («readers») ou de l'élimination («erasers») des adduits ADN- ADP-ribose. Nos données protéomiques ont révélé que les adduits de l'ADN MARylé modulaient sélectivement la reconnaissance de l'ADN par un grand nombre de protéines impliquées dans différentes voies de signalisation cellulaire. Environ 90 protéines, y compris des complexes protéiques, ont été sélectionnées comme lecteurs («readers») potentiels d'adduits ADN-MARylé. Le rôle de l'ADP-ribosylation de l’ADN dans la jonction d'extrémités non homologues (NHEJ) a été partiellement caractérisé dans une étude in vitro. Nous avons démontré que l'ADP-ribosylation de l’extrémité de la cassure double brin («DSB») peut conduire à l'inhibition de la réparation de la DSB bout franc par la voie NHEJ canonique si elle n'est pas éliminée par la glycohydrolase PARG. Au contraire, la présence d'une coupure («nick») proximale avec un site apurinique / apyrimidinique stabilisé conduit à une efficacité NHEJ accrue, apparemment de manière indépendante de l'ADP-ribosylation. Enfin, nous avons recherché de nouveaux inhibiteurs de PARP1, PARP2 et PARP3 parmi les dérivés de 1,4-dihydropyridine, ayant une capacité de liaison à l'ADN. Nos résultats ont révélé que certains analogues de NAD + pourraient être utilisés par les PARPs pour la modification de l'ADN conduisant à la stabilisation des adduits MARylés et PARylés correspondants, en raison de leur résistance à l'activité d'hydrolyse des PARG. Ensemble, ces données mettent en évidence la pertinence physiologique et les résultats biologiques possibles de l’ADP-ribosylation de l’ADN catalysée par les protéines PARPs, tels que la fourniture d'une référence stable de l'emplacement d'une cassure du brin d'ADN sur une carte de chromatine, le recrutement de protéines de réparation de l'ADN et l'inhibition du mécanisme NHEJ toxique DNA-dependent poly(ADP-ribose) polymerases (PARPs) PARP1, PARP2 and PARP3 act as DNA break sensors signaling DNA damage. Upon detecting DNA damage, these PARPs use nicotine adenine dinucleotide as a substrate to synthesize a monomer or polymer of ADP-ribose (MAR or PAR, respectively) covalently attached to the acceptor residue of target proteins. Recently, it was demonstrated that PARP1–3 proteins can directly ADP-ribosylate DNA breaks by attaching MAR and PAR moieties to terminal phosphates. Nevertheless, little is still known about the mechanisms governing substrate recognition and specificity of PARP1, which accounts for most of cellular PARylation activity, as well, about proteins responsible for detection and removal of ADP-ribosylated DNA adducts and its role in multitude of cellular processes.In this study we provide a detailed characterization of PARP1 DNA substrate specificity and mechanisms of DNA PARylation. We showed that the 3′-terminal phosphate residue at double-strand DNA break ends served as a major acceptor site for PARP1-catalysed PARylation depending on the orientation and distance between DNA strand breaks in a single DNA molecule. Moreover, a preference for ADP-ribosylation of DNA molecules containing 3′-terminal phosphate over PARP1 auto-ADP-ribosylation was observed, and a model of DNA modification by PARP1 was proposed. Similar results were obtained with purified recombinant PARP1 and HeLa cell-free extracts. Thus, the biological effects of PARP-mediated ADP-ribosylation may strongly depend on the configuration of complex DNA strand breaks. Furthermore, we elaborated a new research technique to identify and validate proteins responsible for ADP-ribose-DNA adducts detection (“readers”) or removal (“erasers”). Our proteomic data revealed that MARylated DNA adducts selectively modulated DNA recognition of a large number of proteins involved in different cellular pathways. About 90 proteins including protein complexes were selected as potential MAR-DNA adduct readers. The role of DNA ADP-ribosylation in non-homologous end-joining (NHEJ) was partially characterized in an in vitro study. We demonstrated that ADP-ribosylation of DSB terminus can lead to inhibition of blunt DSB repair by canonical NHEJ if not removed by PARG glycohydrolase. Contrary, presence of a proximal nick with a stabilized apurinic/apyrimidinic site leads to increased NHEJ efficiency, apparently in ADP-ribosylation-independent manner. Finally we searched for novel PARP1, PARP2 and PARP3 inhibitors among derivatives of 1,4-dihydropyridine with DNA binding capacity. Our results revealed that some of NAD+ analogues analogs could be used by PARPs for DNA modification leading to stabilization of corresponding MARylated and PARylated adducts due to their PARG hydrolysis activity resistance. Taking together, these data highlight the physiological relevance and possible biological outcomes of PARP-catalyzed DNA-ADP-ribosylation such as providing a stable benchmark of the location of a DNA strand break on a chromatin map, recruitement of DNA repair proteins and inhibition of the toxic NHEJ

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Berglund, Frederick M. "Identification of hnRNP-U as a DNA-PK substrate phosphorylated in response to DNA damage." Thesis, University of Dundee, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505651.

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Wickham, Shelley. "DNA origami : a substrate for the study of molecular motors." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.561126.

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DNA origami is a method for constructing 2-dimensional nanostructures with arbitrary shapes, by folding a long piece of viral genomic DNA into an extended pattern (Rothemund, 2006). In this thesis DNA origami nanostructures that in- corporate active transport are developed, by combining rectangular DNA origami tiles with either synthetic DNA motors, or the protein motor F1-ATPase. The transport of an autonomous, unidirectional, and processive 'burnt-bridges' DNA motor across an extended linear track anchored to a DNA origami tile is demonstrated. Ensemble fluorescence measurements are used to characterise motor transport, and are compared to a simple deterministic model of stepping. The motor moves 100 nm along a track at 0.1 nms-1 Atomic force microscopy (AFM) is used to study the transport of individual motor molecules along the track with single-step resolution. A DNA origami track for a 'two-foot' DNA motor is also developed, and is characterised by AFM and ensemble fluorescence measurements. The burnt-bridges DNA motor is then directed through a track network with either 1 or 3 bifurcations. Ensemble fluorescence measurements demonstrate that the path taken can be controlled by the addition of external control strands, or pre-programmed into the motor. A method for attaching the rotary motor protein F1-ATPase to DNA origami tiles is developed. Different bulk and single-molecule methods for demonstrat- ing protein binding are explored. Single-molecule observations of rotation of the protein motor on a DNA origami substrate are made, and are of equivalent data quality to existing techniques.

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Heale, John-Paul. "Applications of a retroviral integrase towards substrate DNA in vivo." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp03/NQ27159.pdf.

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Howell, Craig A. "Substrate recognition by the yeast Rev1 protein and DNA polymerase ζ". Diss., University of Iowa, 2008. https://ir.uiowa.edu/etd/7.

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DNA damage blocks replication by classical DNA polymerases, those that replicate nondamaged DNA during normal DNA replication and repair, by altering the geometry of the DNA. Consequently, translesion synthesis, the replication of damaged DNA, is catalyzed by non-classical DNA polymerases, which are capable of accommodating the inherent distorted geometry of damaged DNA. The yeast Rev1 protein (Rev1p) specifically catalyzes the incorporation of cytosine opposite template guanine and several types of DNA damage utilizing a unique mechanism of nucleotide selection whereby the sidechain of Arg-324 acts as the template by forming hydrogen bonds with the incoming cytosine. To better understand the impact of this protein-template-directed mechanism on nucleotide incorporation, I carried out pre-steady-state kinetic studies with Rev1p. Interestingly, I found that Rev1p's specificity for incorporating cytosine is achieved solely at the initial nucleotide-binding step. In this respect, Rev1p differs from all previously investigated DNA polymerases. Based on these findings and on structures of another enzyme, MutM, I suggest possible structures for complexes of Rev1p with the other incoming nucleotides. DNA polymerase ζ, encoded by the REV3 gene, functions in the error-prone replication of a wide range of DNA lesions by extending from nucleotides incorporated opposite template lesions by other polymerases. Here I describe genetic and biochemical studies of five yeast DNA polymerase ζ mutant proteins. Four mutant proteins do not complement the rev3Δ mutation, and these proteins have significantly reduced or no polymerase activity relative to the wild-type protein. However, the K1061A protein partially complements the rev3Δ mutation and has nearly normal polymerase activity. Interestingly, the K1061A protein has increased ability to distinguish between correct and incorrect substrates (increased fidelity and decreased misextension ability). These findings have important implications for the mechanism by which this enzyme accommodates distortions in the DNA caused by mismatches and lesions. Additionally, I genetically characterized 21 mutant proteins, which may also affect the substrate specificity of this enzyme. The P962L, L1054A, T1063A, and G1215A mutant proteins were partially capable of complementing the rev3Δ mutation and are candidates for biochemical characterization, as they may have altered substrate specificity.

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DE, CROUY CHANEL AXELLE. "Interaction entre les machines chaperons dnak/dnaj/grpe et groel/groes et leurs proteines substrats." Paris 7, 1997. http://www.theses.fr/1997PA077103.

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Les molecules chaperons forment une classe de proteine qui fixent selectivement les polypeptides naissants, non replies, mal replies, ou agreges, en reconnaissant des regions hydrophobes exposees par les proteines depliees. Cette propriete est la base de l'implication des machines chaperons (dnak/dnaj/grpe) et (groel/groes) dans des processus cellulaires tels que le repliement, l'adressage, la renaturation des proteines, et le controle des interactions proteine-proteine. Les chaperons fonctionnent en collaboration avec leur cochaperon. Nous avons etudie l'interaction entre les machines chaperons d'e. Coli et leurs substrats proteiques et l'effet produit par la presence des cochaperons. Groes diminue la specificite de groel pour les acides amines hydrophobes et augmente celle pour les acides amines hydrophiles. Dnaj attenue les sites hydrophobes de dnak cependant qu'il renforce le site arg/lys. Par ailleurs, dnaj augmente significativement l'interaction entre dnak et les peptides en helice. Au contraire des hsp90 qui semblent interagir avec de nombreuses proteines natives, dnak et groel interagissent principalement avec des proteines depliees. Cependant, nous avons montre que dnak et groel interagissent plus frequemment qu'on ne le suppose avec les proteines natives. L'affinite de dnak est en correlation avec l'hydrophobicite de surface des proteines natives. Nous avons etudie l'interaction entre dnak et les proteines membranaires, et nous avons montre que dnak interagit fortement avec les proteines membranaires solubilisees et beaucoup moins avec celles inserees dans les membranes. Enfin, dans une etude in vitro, nous avons montre que dnaj presente une activite proteine disulfure isomerase. Et nous presentons en plus, un travail portant sur l'expression et l'etat d'oxydoreduction des proteines d'e. Coli dans des mutants redox et notamment des mutants de dnaj.

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Nandakumar, Jayakrishnan. "Discrimination of RNA versus DNA by an RNA ligase and distinct modes of substrate recognition by DNA ligases /." Access full-text from WCMC:, 2007. http://proquest.umi.com/pqdweb?did=1428838891&sid=13&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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Hurley, Eldon Kenneth Jr. "Photolyase: Its Damaged DNA Substrate and Amino Acid Radical Formation During Photorepair." Thesis, Virginia Tech, 2005. http://hdl.handle.net/10919/31084.

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Ultraviolet light damages genomic material by inducing the formation of covalent bonds between adjacent pyrimidines. Cis-syn cyclobutane pyrimidine dimers (CPD)constitute the most abundant primary lesion in DNA. Photolyase, a light-activated enzyme, catalytically repairs these lesions. Although many steps in the photolyase-mediated repair process have been mapped, details of the mechanism remain cryptic. Difference FT-IR spectroscopy was employed to obtain new mechanistic information about photorepair. Purified oligonucleotides, containing a central diuracil, dithymidine, or cyclobutane thymidine dimer, were monitored using vibrational methods. Construction of difference infrared data between undamaged and damaged DNA permitted examination of nucleic acid changes upon formation of the CPD lesion; these experiments indicated that C=O and C-H frequencies can be used as markers for DNA damage. Furthermore, in purified photolyase containing isotopically-labeled aromatic amino acids, we observed that tryptophan residues in photolyase underwent structural changes during photorepair. These data indicate that electron transfer during DNA repair occurs through-bond, and that redox-active, aromatic residues form the pathway for electron transfer. Master of Science

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Bellamy, Stuart Robert William. "A kinetic analysis of substrate recognition by uracil DNA glycosylase from herpes simplex virus type 1." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.250977.

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Vallur, Aarthy C. "Kinetic analysis of the contribution of base flipping to the substrate specificity and catalytic activity of human alkyladenine dna glycosylase." [Gainesville, Fla.] : University of Florida, 2004. http://purl.fcla.edu/fcla/etd/UFE0008300.

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Thesis (Ph.D.)--University of Florida, 2004. Typescript. Title from title page of source document. Document formatted into pages; contains 135 pages. Includes Vita. Includes bibliographical references.

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Rettich, Jan [Verfasser], and Andrea [Akademischer Betreuer] Pichler. "Characterisation of the DNA endonuclease subunit EME1 as novel substrate of sumoylated Ubc9." Freiburg : Universität, 2016. http://d-nb.info/1150164506/34.

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D'Abbadie, Marc François. "Directed evolution of polymerases with altered substrate specificities : the paradigm of ancient DNA." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613870.

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Alves, D. "Studies into the structure of human telomerase and the utilisation of its DNA substrate." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.595488.

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Human telomerase is minimally composed of protein (hTERT) and RNA (hTR) components, although information regarding the stoichiometry of these moieties within the active enzyme remains undetermined. The low natural abundance of human telomerase, coupled with poor levels of in vitro expression has limited the use of classical biophysical approaches to gain such structural insights. Initial work within this thesis describes the use of a single-molecule fluorescence technique employing two-colour coincidence detection (TCCD) to directly observe and characterise the complex formed between fluorescently-labelled hTERT, hTR and telomeric substrate DNA components. It was found that catalytically active human telomerase comprises a kinetically-stable complex between one hTERT and one hTR component, which in turn recruits just one substrate DNA moiety. The interaction between telomerase and its DNA substrate is dependent upon a number of factors. Chapter 3 describes the substrate’s potential to form non-classical four-stranded DNA structures called G-quadruplexes, and the use of agents that stabilise such structures to perturb the substrate’s utilisation by telomerase. A method for directly assessing telomerase activity in vitro was developed and used to demonstrate that a quinoline-based G-quadruplex-binding macrocycle was capable of regulating telomerase activity. Other factors that have potential roles in the control of substrate-binding are the chaperone proteins Hsp90 and p23. Initial efforts to elucidate any such effects are described in Chapter 4, with the demonstration that telomerase activity in wheat germ lysate could be stimulated through the addition of p23 forming a firm basis for future study.

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Kumar, Sandeep. "Biochemical, Mechanistic, and Structural Characterization of DNA Polymerase X from African Swine Fever Virus." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1211380265.

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Sekerina, Elena. "Das humane Parvulin 14: Struktur und Untersuchungen an Substrat- und DNA-Komplexen." [S.l.] : [s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=964312719.

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Kraynov, Vadim S. "Structural basis for the catalytic efficiency, processivity, substrate specificity and fidelity of DNA polymerase beta /." The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487950153602297.

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39

Yu, Zhen. "Substrate-Selective Copper Catalysts as Catalytic Metallodrugs: from G-Quadruplex Targeting Small-Molecular Nucleases to Artificial Glycosidases." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1500316480959497.

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40

Guo, Shuangli. "ROLE OF REPLICATION PROTEIN A (RPA) AND PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) IN DNA MISMATCH REPAIR." UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_diss/258.

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PCNA and RPA are required for DNA mismatch repair (MMR), but their rolesin the pathway are not fully understood. Using an affinity pull-down approach, weshow that (1) increased PCNA binding to DNA heteroduplexes is associated withthe appearance and accumulation of excision products; and (2) RPAphosphorylation occurs when DNA polymerase ?? binds to the DNA substrate. Wetherefore hypothesize that PCNA plays an important role in mismatch-provokedexcision and that RPA phosphorylation plays an important role in DNA resynthesis.To determine the role of PCNA in MMR, mismatch-provoked and nick-directedexcision was assayed in a cell-free system in the presence of the PCNA inhibitor,p21CIP1/WAF. We show that whereas PCNA is essential for 3' directed excision, it isdispensable for the 5' directed reaction, suggesting a differential role for PCNA inMMR. We further find that the PCNA-dependent pathway is the only pathway for3' directed excision, but there are at least two pathways for 5' directed excision,one of which is a PCNA-independent 5' excision pathway. To determine if RPAphosphorylation facilitates DNA resynthesis, a gap-filling assay was developedusing both a cell-free system and a purified system, and we demonstrate that RPAphosphorylation stimulates DNA polymerase ??-catalyzed resynthesis in bothsystems. Kinetic studies indicate that phosphorylated RPA has a lower affinity forDNA compared with un-phosphorylated RPA. Therefore, the stimulation ofresynthesis by phosphorylated RPA is likely due to the fact that phosphorylationpromotes the release of RPA from DNA, thereby making DNA template availablefor resynthesis.

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Hou, Shurong. "Structural Mechanism of Substrate Specificity In Human Cytidine Deaminase Family APOBEC3s." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1079.

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APOBEC3s (A3s) are a family of human cytidine deaminases that play important roles in both innate immunity and cancer. A3s protect host cells against retroviruses and retrotransposons by deaminating cytosine to uracil on foreign pathogenic genomes. However, when mis-regulated, A3s can cause heterogeneities in host genome and thus promote cancer and the development of therapeutic resistance. The family consists of seven members with either one (A3A, A3C and A3H) or two zinc-binding domains (A3B, A3D, A3D and A3G). Despite overall similarity, A3 proteins have distinct deamination activity and substrate specificity. Over the past years, several crystal and NMR structures of apo A3s and DNA/RNA-bound A3s have been determined. These structures have suggested the importance of the loops around the active site for nucleotide specificity and binding. However, the structural mechanism underlying A3 activity and substrate specificity requires further examination. Using a combination of computational molecular modeling and parallel molecular dynamics (pMD) simulations followed by experimental verifications, I investigated the roles of active site residues and surrounding loops in determining the substrate specificity and RNA versus DNA binding among A3s. Starting with A3B, I revealed the structural basis and gatekeeper residue for DNA binding. I also identified a unique auto-inhibited conformation in A3B that restricts access to the active site and may underlie lower catalytic activity compared to the highly similar A3A. Besides, I investigated the structural mechanism of substrate specificity and ssDNA binding conformation in A3s. I found an interdependence between substrate conformation and specificity. Specifically, the linear DNA conformation helps accommodate CC dinucleotide motif while the U-shaped conformation prefers TC. I also identified the molecular mechanisms of substrate sequence specificity at -1’ and -2’ positions. Characterization of substrate binding to A3A revealed that intra-DNA interactions may be responsible for the specificity in A3A. Finally, I investigated the structural mechanism for exclusion of RNA from A3G catalytic activity using similar methods. Overall, the comprehensive analysis of A3s in this thesis shed light into the structural mechanism of substrate specificity and broaden the understanding of molecular interactions underlying the biological function of these enzymes. These results have implications for designing specific A3 inhibitors as well as base editing systems for gene therapy.

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Liu, Jia. "Substrate stereoselectivity, kinetic mechanism and structure-function studies of Rat DNA Polymerase [beta] via pre-steady-state kinetics /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486399451961026.

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43

Kurtovic, Sanela. "Directed Evolution of Glutathione Transferases Guided by Multivariate Data Analysis." Doctoral thesis, Uppsala University, Department of Biochemistry and Organic Chemistry, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8718.

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Evolution of enzymes with novel functional properties has gained much attention in recent years. Naturally evolved enzymes are adapted to work in living cells under physiological conditions, circumstances that are not always available for industrial processes calling for novel and better catalysts. Furthermore, altering enzyme function also affords insight into how enzymes work and how natural evolution operates. Previous investigations have explored catalytic properties in the directed evolution of mutant libraries with high sequence variation. Before this study was initiated, functional analysis of mutant libraries was, to a large extent, restricted to uni- or bivariate methods. Consequently, there was a need to apply multivariate data analysis (MVA) techniques in this context. Directed evolution was approached by DNA shuffling of glutathione transferases (GSTs) in this thesis. GSTs are multifarious enzymes that have detoxication of both exo- and endogenous compounds as their primary function. They catalyze the nucleophilic attack by the tripeptide glutathione on many different electrophilic substrates. Several multivariate analysis tools, e.g. principal component (PC), hierarchical cluster, and K-means cluster analyses, were applied to large mutant libraries assayed with a battery of GST substrates. By this approach, evolvable units (quasi-species) fit for further evolution were identified. It was clear that different substrates undergoing different kinds of chemical transformation can group together in a multi-dimensional substrate-activity space, thus being responsible for a certain quasi-species cluster. Furthermore, the importance of the chemical environment, or substrate matrix, in enzyme evolution was recognized. Diverging substrate selectivity profiles among homologous enzymes acting on substrates performing the same kind of chemistry were identified by MVA. Important structure-function activity relationships with the prodrug azathioprine were elucidated by segment analysis of a shuffled GST mutant library. Together, these results illustrate important methods applied to molecular enzyme evolution.

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Paquette, Sarah-Jo. "Control of substrate utilization by O-islands and S-loops in Escherichia coli O157:H7." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, c2011, 2011. http://hdl.handle.net/10133/3104.

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Escherichia coli O157:H7 is an enteric pathogen that can cause severe gastrointestinal disease, sometimes leading to hospitalization and death. These bacteria have a variety of virulence factors that can be encoded for on pathogenicity islands (PAIs). The goal of this study was to characterize specific E. coli O157:H7 PAI deletion mutants using three methods: Phentotype Microarrays (PM), growth curves and survival curves were used to elucidate possible roles for the PAIs. Results from the PM study suggest that PAIs have a role in carbon substrate utilization; i.e., four of the O-island (OI) deletion mutants (OI-87, 98, 102 and 172) and an S-Loop (SL-72) deletion mutant exhibited differences in substrate utilization (gains and losses in utilization) compared to parental O157:H7 strains EDL933 (OI) and Sakai (SL), respectively. All of the mutants with the exception of the OI-135 mutant exhibited differences in level of substrate utilization for substrates shown to have important roles in the bacterium. Cell growth results showed that three OI deletion mutants (OI-55, 87 and 102) and the SL (SL-72) mutant exhibited a difference in rate of growth compared to the parental strains. Cell viability results showed that seven of the OI deletion mutants (OI-51, 55, 98, 108, 135, 172 and 176) exhibited different rates of decline in cell number when transferred to sterile water compared to the parental strain. The results show that removal of PAIs from E. coli O157:H7 can affect carbon utilization, growth and survival demonstrating the importance of PAIs in the ecology of these bacteria. xx, 208 leaves : ill. (some col.) ; 29 cm

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Butryn, Agata Anna [Verfasser], and Roland [Akademischer Betreuer] Beckmann. "Structural characterization of the Swi2/Snf2 ATPase Mot1 in complex with protein and DNA substrate / Agata Anna Butryn. Betreuer: Roland Beckmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2015. http://d-nb.info/1076981259/34.

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Siegmund, Vanessa [Verfasser]. "DNA and RNA Polymerases with Expanded Substrate Scope : Synthesis of Modified Nucleic Acids Using Engineered Polymerases Generated by Directed Evolution / Vanessa Siegmund." Konstanz : Bibliothek der Universität Konstanz, 2013. http://d-nb.info/1043443320/34.

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Galal, Wiebke [Verfasser]. "Working towards understanding DNA replication : coupling of a 3'-5' helicase with a replicative polymerase on a rolling circle substrate / Wiebke Galal." Konstanz : Bibliothek der Universität Konstanz, 2012. http://d-nb.info/1027269273/34.

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Jin, Yi. "Studies to characterize the requirements for the binding and release of ERdj3 a mammalian ER DnaJ homolog from substrates /." View the abstract Download the full-text PDF version, 2008. http://etd.utmem.edu/ABSTRACTS/2008-040-Jin-index.htm.

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Thesis (Ph.D.)--University of Tennessee Health Science Center, 2008. Title from title page screen (viewed on February 9, 2009). Research advisor: Linda M. Hendershot, Ph.D. Document formatted into pages (ix, 90 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 67-82).

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Subramaniam, Srisunder. "Studies of conformational changes and dynamics accompanying substrate recognition, allostery and catalysis in bacteriophage lambda integrase." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111655332.

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Dressler, Alina [Verfasser], and Hemmo [Akademischer Betreuer] Meyer. "The AAA-ATPase p97 and its cofactors in regulatory degradation of substrate proteins after DNA damage or replication stress / Alina Dressler ; Betreuer: Hemmo Meyer." Duisburg, 2016. http://d-nb.info/1116941848/34.

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Dissertations / Theses on the topic 'DNA Substrates'

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