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Dissertations / Theses on the topic 'DNA hydrolysis'
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1
Evans, Steven John. "Structure, function and mechanism of action of bovine pancreatic deoxyribonuclease I : role of amino acid residues involved in phosphate contacts." Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321857.
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Przybylski, Jennifer L., and University of Lethbridge Faculty of Arts and Science. "Computational modeling of the hydrolysis of 2'-deoxyribonucleic acids." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, c2009, 2009. http://hdl.handle.net/10133/1292.
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The mechanism for the hydrolysis of 2′-deoxyribonucleosides is examined using computational chemistry techniques. Initially, a model capable of accurately predicting the mechanism and activation barrier for the uncatalyzed hydrolysis of 2′-deoxyuridine is designed. It is found that the smallest model includes both explicit and implicit solvation during the optimization step. Next, this hybrid solvation model is applied to four natural nucleosides, namely 2′-deoxyadenosine, 2′-deoxycytidine, 2′-deoxyguanosine and thymidine. The hybrid model correctly predicts the trend in activation Gibbs energies for the pyrimidines and purines, separately. Finally, the concepts developed during the generation of the uncatalyzed hydrolysis model are applied to the mechanism of action of a glycosylase enzyme, namely human uracil DNA glycosylase. A hybrid ONIOM approach is utilized to study the experimentally proposed two-step mechanism. Results regarding the protonation state of His148 are inconclusive, and future directions are proposed.xiii, [131] leaves : ill. (some col.) ; 29 cm
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Eissa, Omaima Abdel-Latif Elkotb. "Cloning of a novel operon containing genes for 4-#alpha#-glucanotransferase, maltodextrin phosphorylase, and a regulatory protein from Clostridium butyricum." Thesis, University of Southampton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296246.
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Marrone, April. "THE BIOCHEMICAL REACTIONS OF DRY STATE DNA." Doctoral diss., University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3622.
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The biochemistry of dry state DNA is of interest to the fields of forensics, ancient DNA, and DNA storage. The exact chemical nature of the degradation of the DNA molecule in the dry state has not been studied prior. If determined what chemical changes the DNA molecule undergoes, to what degree and in what time frame then protocols can be implemented to bypass the impact of this damage or to repair it when necessary. It is suspected that similar reactions occur to the dry state DNA molecule as does to the hydrated molecule. It cannot be assumed, however that these types of chemical processes occur to the same extent and at the same rates. In general the generic process of hydrolysis encompasses two important reactions, that of deamination and of base loss from the 2’-deoxyribose backbone. Base loss is believed to ultimately lead to chain scission. It is also suspect that reactive oxygen species (ROS) have an important role in the chemistry associated with DNA. Species such as hydroxyl radicals (OH·) and singlet oxygen (¹O₂) can lead to strand scissions and chemically modified bases. Throughout this project various techniques were used to determine damage to DNA and its molecular constituents under conditions leading to hydrolytic and oxidative damage. Novel techniques used in this study include ion-pairing chromatography and denaturing HPLC (DHPLC) to measure glycosidic bond cleavage and strand breaks. The extent to which the macromolecule haemoglobin (Hb) can lead to oxidative damage of DNA in dried blood stains by acting as a Fenton chemistry catalyst was evaluated. Additionally the enzymatic activity of the extracellular nuclease from Alteromonas espejiana, BAL 31 was studied as it pertains to the degradation of single-stranded short homopolymeric oligonucleotides. This study serves as the basis for future, more in depth experimentation into the more specific nature of dry state DNA biochemistry.
It was found that to a large extent the same degradation reactions (base hydrolysis, base modifications, and strand breaks) do occur in the dry state as in the hydrated state when heat and UV radiation are used as energy sources. Reaction rates indicate that base hydrolysis and deamination occur much more slowly, yet have the same energies of activation in both states. Single strand breaks of dry state duplex DNA occur with a half life of 24 ± 2 days and appears to occur in a mechanistic manner which could be of interest when attempting to repair such damage. In addition, base loss alone does not correlate with the extent of single strand breaks detected. Thermodynamic data can lead to the conclusion that DNA degradation in both dry and hydrated states is not a spontaneous process. It is also concluded that though the Hb molecule undergoes oxidative changes over time, these changes do not impact its ability to become a more aggressive Fenton reagent. However, the presence of Hb in the vicinity of DNA does create the opportunity for OH· induced damage to the deoxyribose sugar, and most likely the DNA bases themselves. This study also reveals that the general purpose BAL 31 nuclease commonly used in molecular genetics exhibits a hithertofore non-characterized degree of substrate specificity with respect to single-stranded DNA oligomers. Specifically, BAL 31 nuclease activity was found to be affected by the presence of guanine in ssDNA oligomers.Ph.D.
Department of Chemistry
Sciences
Chemistry PhD
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Bhat, Anayat [Verfasser]. "Live Cell Fluorescence Imaging of Nucleotide Dynamics : ATP Hydrolysis and DNA Damage Response / Anayat Bhat." Konstanz : KOPS Universität Konstanz, 2021. http://d-nb.info/1229351094/34.
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Marin, Córdoba Roberto. "Chromium carcinogenesis characterization of DNA damaging intermediates by EPR ³¹P NMR, HPLC, ESI-MS and magnetic susceptibility /." Ohio : Ohio University, 2010. http://www.ohiolink.edu/etd/view.cgi?ohiou1261417590.
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Moysan-Le, Meur Annie. "Caracterisation de dosage des produits de photoaddition de psoralene dans l'adn "in vitro" et dans l'adn cellulaire." Paris 6, 1987. http://www.theses.fr/1987PA066021.
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Marin, Cordoba Roberto. "Chromium Carcinogenesis: Characterization of DNA damaging Intermediates by EPR 31P NMR, HPLC, ESI-MS and Magnetic Susceptibility." Ohio University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1261417590.
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Taori, Vijay P. "Poly(glycoamidoamine)s: Understanding their Structure and Structure-Bioactivity Relationships." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77982.
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In order to achieve efficient therapeutic effect, it is important to understand the structure of biomaterials that are used in the therapeutic delivery system. This dissertation is dedicated towards understanding the hydrolysis pattern of plasmid DNA (pDNA) delivery vehicles comprised of poly(glycoamidoamine)s (PGAAs) under physiological conditions and effects of subtle changes in the chemical structure of the PGAAs on its biological performance.
The unusual hydrolysis of the tartarate and galactarate based PGAAs was investigated by studying the hydrolysis of small model molecules which mimic the repeat unit of the respective polymers. In the case of galactarate and tartarate based molecules with terminal amines showed faster hydrolysis of the amide bonds. In addition for the tartarate based compounds, it was also found that it is necessary to have terminal amine functionality for the intramolecular hydrolysis to occur. The model compounds consists of two amide bonds and were designed symmetric, however amide bond on only one side of the tartarate moiety show underwent hydrolysis. Further studies show that one side of the amine assists the hydrolysis of the amide bond on the other side of the tartarate moiety.
The degradation of poly(L-tartaramidopentaethylenetetramine) (T4) was also used to study the sustained release of pDNA from the layer-by-layer constructs of T4/pDNA. The thickness of the constructs was characterized by ellipsometry while the UV-visible spectroscopy was used to characterize the loading capacity of the constructs for pDNA. The indirect sustained release of pDNA under the physiological conditions with respect to time was characterized by the cellular uptake studies in HeLa cells. The increase in the uptake of the Cy5 labeled pDNA was seen at extended period of eleven days. The integrity of the sustained released pDNA for the transgene expression was characterized with an assay to see the expression of the green fluorescent protein (GFP) from the T4/GFP-pDNA layer-by-layer constructs.
PGAAs show a very efficient delivery of the pDNA in a non-toxic manner. The chemical structure of the polymer can dictate the binding with pDNA and also the release of the pDNA form the polymer-pDNA complexes. In order to better understand the fundamentals of the nucleic acid delivery and to better design the nucleic acid delivery vehicles, subtle changes in the chemical structure of the PGAAs were designed and studied for the biological activity. The effect of charge type was investigated by designing and synthesizing guanidine based polymer series analogues to galactarate and tartarate based PGAAs (G1 and T1) which incorporate secondary amines as the charge type on the polymer backbone. The guanidine based polymer series, poly(glycoamidoguanidine)s (PGAGs), show very non toxic behavior in HeLa cells at all the different polymer to pDNA ratio (N/P ratio) studied. Interestingly PGAGs are the only non-toxic guanidine containing polymers which are reported in the literature to the date. The cellular uptake of pDNA assisted from the PGAGs is a little higher than PGAAs compared although both the series of polymers show similar transgene expression. The transgene expression in case of PGAGs also imply the release of the polymer-pDNA complexes from the endosome. In another study of structure-bioactivity relationship based on the degree of polymerization (DP) of poly(galactaramidopentaethylenetetramine) (G4), it was found that the increase in the DP of G4 increases the toxicity of the polymers in the HeLa cells.Ph. D.
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Incardona, Marie-Françoise. "Mesure de lésions de type oxydatif de l'ADN dans les fluides biologiques et dans l'ADN isolé." Grenoble 1, 1994. http://www.theses.fr/1994GRE10162.
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Divers facteurs (stress oxydant, exposition a divers rayonnements) peuvent engendrer des modifications des bases de l'adn. La mise au point de methodes d'analyse suffisamment fiables et sensibles nous a permis de detecter et de doser plusieurs dommages oxydatifs dans un fluide biologique (urine humaine) et dans l'adn isole. Pour cela, deux techniques ont ete respectivement mises en uvre: la chromatographie gazeuse couplee a la spectrometrie de masse (cg/sm) et la chromatographie liquide a haute performance associee a une detection electrochimique (clhp/ec). La mise au point de methodes de detection de dommages oxydatifs dans l'urine par cg/sm a ete appliquee a la 5-hydroxymethyluracile, la 5-hydroxyuracile et a leurs nucleosides. Ce travail a implique, la synthese d'etalons internes enrichis isotopiquement (#2h, #1#5n, #1#8o) pour une mesure quantitative des lesions, la mise au point de la technique d'extraction du defaut et enfin l'optimisation des parametres de cg/sm pour l'obtention d'une reponse optimale. Un deuxieme volet du travail a concerne le developpement d'une nouvelle methode d'analyse de bases modifiees utilisant une colonne chromatographique a phase normale (nh#2) couplee a un detecteur electrochimique. Celle-ci nous a permis de detecter plusieurs molecules hydrophiles (5-hydroxyuracile, 5-hydroxycytosine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine et 4,6-diamino-5-formamidopyrimidine) jusqu'a present difficiles a mesurer dans les conditions usuelles (colonne c18). Nous avons applique cet outil a la recherche et au dosage de la 5-hydroxyuracile et de la 5-hydroxycytosine dans l'adn soumis a deux conditions de stress oxydant (radiations ionisantes et photooxydation sensibilisee). La recherche de ces bases oxydees dans l'adn a ete facilitee par une nouvelle methode d'hydrolyse
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Zhou, Rong. "Topoisomerase II and drug resistance in leukemic cells /." Stockholm, 2001. http://diss.kib.ki.se/2001/91-628-4738-4/.
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Al-Sayed, Mahmoud Kassem. "Extraction, fractionnement et caractérisation des lipides polyinsaturés d'oeufs de la truite arc-en-ciel (Oncorhynchus mykiss)." Thesis, Vandoeuvre-les-Nancy, INPL, 2007. http://www.theses.fr/2007INPL087N/document.
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Parmi les œufs de poisson, qui sont une ressource aquatique nutritionnelle intéressante, ceux de la truite arc-en-ciel (Oncorhynchus mykiss) contiennent une quantité élevée de protéines et une huile riche en acides gras polyinsaturés (AGPI), avec une proportion très importante de phospholipides. Cependant, l’œuf de poisson présente une capacité élevée d’auto-protection contre les contraintes extérieures, qui limite la destructuration de son réseau protéique par attaque enzymatique. Ainsi, le degré d’hydrolyse des œufs de la truite l’Alcalase®, la Neutrase® et la Protamex® varie entre 3 et 7 %, ce qui est très faible (20 % dans la majorité des protéines animales). L’extraction des lipides après protéolyse partielle est incomplète, probablement en raison d’interactions fortes avec les protéines faiblement hydrolysées. Ils contiennent une teneur élevée en phospholipides (53 % des lipides totaux) et les acides gras polyinsaturés entrent pour 42 % des acides gras totaux. Les AGPI, notamment le DHA, sont situés préférentiellement en position sn-2 sur la molécule de glycérol ce qui est particulièrement intéressant du point de vue nutritionnel. La stabilité à l’oxydation de l’huile a été étudiée par diverses méthodes, dont la spectrométrie infrarouge à transformée de Fourier. Cette méthode s’est avérée extrêmement intéressante pour une analyse structurale de la dégradation de l’huile en cours d’oxydation. Il peut être conclu que les lipides tirés des œufs de la truite arc-en-ciel ou de poisson en général, ont un réel avenir en matière de complément alimentaire ou nutraceutique, à condition de lever l’obstacle de l’hydrolyse enzymatique des protéines du chorion et du vitellusFish eggs, especially those of the rainbow trout (Oncorhynchus mykiss) in the present study, are an interesting nutritional aquatic source. They contain proteins of high value, as well as an oil rich in polyunsaturated fatty acids (PUFA) with a large percentage of phospholipids. However, they exhibit a high auto-protection capacity against environmental constraints and thus, the degree of hydrolysis of rainbow trout eggs by Alcalase®, Neutrase® and Protamex® proteases varied solely within 3-7 %. This value was low compared with the 20 % obtained in most animal proteins. The phospholipid content was high (53 % of total lipids) and PUFA accounted for 42 % of total fatty acids. Among PUFA, DHA was found preferably at the sn-2 position of the glycerol backbone, which is of special interest about nutritional properties. The oil release by enzymatic hydrolysis was found limited compared with chemical methods, probably because of the strong interactions engaged with the incomplete destructured protein network. The oxidative stability of the oil was studied through several methods in which the infrared Fourier transform appeared as the best tool for structural analysis along the oxidation process. As a conclusion, lipids from fish eggs, especially from rainbow trout, could be a nutritional breakthrough, as far the enzymatic hydrolysis of the vitellus and of the chorion proteins is achieved
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Maester, Thais Carvalho. "Prospecção de sequências genômicas codificadoras de enzimas lipolíticas degradadoras de hidrocarbonetos de petróleo." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-15092011-151851/.
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Enzimas lipolíticas possuem enorme potencial biotecnológico. O objetivo foi prospectar genes para a codificação de enzimas lipolíticas em biblioteca metagenômica com 4224 clones. A atividade lipolítica foi avaliada pela formação de halo ao redor das colônias através do cultivo dos clones em meio de cultura suplementado com tributirina, sendo positiva para 30 clones, e dois foram selecionados e tiveram o DNA sub-clonado. Os DNAs das sub-bibliotecas foram sequenciados, gerando um contig completo para o clone PL28.F10, que foi comparado com as sequências do banco NCBI. Uma ORF codificadora de esterase/lipase de 303 aminoácidos e 61% de identidade com micro-organismo não cultivável foi encontrada. Árvores filogenéticas indicam que o clone possui a ORF15 mais próxima da família IV das esterases/lipases. Foi possível identificar os sítios ativos representativos da família, confirmando o resultado das árvores filogenéticas. Com sequências já patenteadas, a ORF15 é um grupo irmão das sequências de esterases/lipases da BASF e de uma proteína não identificada da CAMBIA.Lipolytic enzymes have show enormous biotechnological potential. The work was done to find genes which codify lipolytic enzymes in a metagenomic library with 4224 clones. Clones were selected according to lipolytic activity and were assessed by cultivation in medium supplemented with tributyrin. Assessment was done by observation of halos formed around the colonies, with 30 clones producing halos. Of these, two were selected. DNA from the sub libraries was sequenced, generating a complete contig for clone PL28.F10 that was compared to sequences from the NCBI. An ORF of 303 amino acids with 61% of identity with uncunturable microorganism were found. The clone presented the ORF15 similar to that of lipolytic enzyme family IV. The alignments made possible the identification of active sites which represent the family, confirming the results obtained with the construction of the cladograms. The ORF15 showed similarities to patented BASF esterase/lipase and an unnamed protein of CAMBIA.
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Sioud, Mouldy. "Etude des mecanismes moleculaires d'action des inhibiteurs des adn topoisomerases 2 chez les archaebacteries halophiles." Paris 7, 1988. http://www.theses.fr/1988PA077155.
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Pommier, Yves. "Les agents intercalants affectent le fonctionnement des adn topoisomerases deux eukaryotes." Paris 6, 1986. http://www.theses.fr/1986PA066570.
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Parmi les medicaments anticancereux les plus actifs, les agents intercalants de l'adn (anthracyclines, acridines) produisent des lesions sur l'adn de type soit cassure du dna, soit pontage adn-proteine. Ces alterations sont analysees par elution alcaline, sedimentation de nucleotide et sedimentation alcaline. Ces lesions sont reversibles apres suppression des intercalants (culture cellulaire, cellules leuconiques(l1210)). Les dna topoisomerase 2 (enzyme de replication, de transcription, d'organisation de chromatine) sont responsables des lesions provoquees par les agents intercalants du dna, car dans ces conditions, elles forment les ponts proteine-dna. L'utilisation des cellules soit sensibles soit resistantes aux inhibiteurs de dna topoisomerase 2 a permis de mettre en evidence leur role dans la formation de ces alterations au dna
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Volff, Jean-Nicolas. "Stimulation de l'instabilité génétique et des réarrangements génomiques chez streptomyces ambofaciens." Nancy 1, 1994. http://www.theses.fr/1994NAN10008.
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L’instabilité génétique de la bactérie streptomyces ambofaciens atcc23877 se manifeste par l'apparition de mutants dépigmentés à une fréquence voisine de 0,5%. Certains mutants sont pléiotropes. La majorité des mutants dépigmentés présentent des délétions et des amplifications de grandes séquences d’ADN. Deux mutants présentant une instabilité génétique augmentée ont été isoles. Les rayonnements ultraviolets, la mitomycine c et l'acide nitreux augmentent la fréquence des mutants dépigmentés. De plus, cinq antibiotiques inhibant l'ADN gyrase, la topoisomérase ii bactérienne, induisent de nombreux secteurs mutants (phénotype patchwork). La fréquence des mutants dépigmentés induits peut atteindre des valeurs proches de 100%. Ces mutants présentent les mêmes caractéristiques que les spontanés. Par contre, la rifampicine, inhibant la transcription, et la streptomycine, agissant au niveau de la traduction, n'ont aucun effet sur le phénomène. Des mutants résistants à la novobiocine ou à l'acide oxolinique ont été isolés. Chez ceux-ci, ces antibiotiques n'induisent plus l'instabilité génétique. D’autre part, les gènes codant les deux sous-unités de la gyrase ont été clonés, partiellement séquences et localises proches du gène DNAA et de l'origine de réplication chromosomique ORIC. L’intervention dans le phénomène de fonctions inductibles de type SOS ou de cassures double-brins est discutée. De plus, un nouveau mécanisme de plasticité génomique impliquant l’ADN gyrase est provoqué
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Amir, Aslani Arsia. "Étude des propriétés structurales d'un site de coupure préférentiel de la topoisomerase II." Paris 6, 1996. http://www.theses.fr/1996PA066454.
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La grande variete des structures d'adn repertoriees, nous permet de penser que ce sont les proprietes conformationnelles de l'adn qui se trouvent a la base des evenements gouvernant la regulation genetique. A l'origine de celle-ci se trouvent les phenomenes de reconnaissance moleculaires : liaison d'un ligand, que ce soit une proteine ou un agent antitumoral, a un domaine particulier de l'adn. L'analyse des sequences au voisinage des principaux sites de clivage de l'adn de pbr322 par la topoisomerase ii de thymus de veau couplee a l'ellipticine a permis de mettre en evidence une sequence consensus dont le prototype est le site (fort) 22 (fosse et al. , 1991). Cette coupure est egalement stimulee par l'etoposide vp-16 qui est sense agir sur la topoisomerase ii par un mecanisme different de celui de l'ellipticine. La question est de savoir si le site de coupure 22 de la topoisomerase ii peut adopter une conformation differente de celle de la double helice lineaire ? au cas ou une telle conformation existe, est-elle un site de reconnaissance pour la topoisomerase ii couplee aux principaux agents antitumoraux ? la sequence comprenant le site 22, 5'-d(agcttatc-atc-gtattgct)-3' (-atc-) et 5'-d(agcttatc-gat-gtattgct)-3' (-gat-) de par sa symetrie, est susceptible d'adopter une structure repliee cruciforme probablement en equilibre avec la structure en duplex lineaire. Pour analyser un tel systeme, nous avons utilise les techniques de resonance magnetique multinucleaire (#1h et #31p) et multidimensionnelle (1d, 2d) combinees a celles d'absorption-uv et de dichroisme circulaire (dc). Chaque brin a ete etudie independamment. Nous montrons que le brin -atc- adopte une structure exclusivement en epingle a cheveux, tandis que le brin -gat- est present sous forme d'un equilibre monomere-dimere, ou le monomere (forme repliee en epingle a cheveux) est preponderant. La mesure de la thermostabilite des formes en epingle a cheveux -gat- et -atc- montre que -atc- est plus stable que -gat- de 4c. Ceci est en accord avec les spectres de dc qui indiquent que les interactions d'empilement sont plus importantes dans -atc- que dans -gat-. Les spectres de rmn noesy montrent que le reseau des interactions noes est identique dans la tige des deux oligonucleotides mais les connectivites interresiduelles sont bien plus nombreuses dans la boucle -atc- que dans -gat-. Des experiences #1h-#31 cosy avec detection proton ou #31p-#1h (doc) ont ete realisees dans le but d'etudier la conformation du squelette phosphodiester des brins -atc- et -gat-. Pour -atc- des distorsions du squelette phosphodiester se produisent, sur l'ensemble de la boucle, alors que dans le cas de -gat- elles apparaissent beaucoup plus faibles en conclusion, il est necessaire de souligner la convergence des resultats obtenus avec des approches tres diverses : rmn, dichroisme circulaire mecanique moleculaire. La capacite de chaque brin -atc- et -gat- d'adopter une structure repliee est en faveur d'un equilibre conformationnel dans le site 22, in vivo. Ce dernier est certainement necessaire a la reconnaissance de l'adn par les enzymes telles que la topoisomerase ii.
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VILAREM, PUIG MARIE-JOSE. "Etude des mecanismes d'activite cytotoxique et moleculaire du bd-40, une aza-ellipticine douee de pouvoir antitumoral." Paris 6, 1987. http://www.theses.fr/1987PA066219.
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Charcosset, Jean-Yves. "Etude sur le mécanisme d'action de dérivés de l'ellipticine sur des cellules en culture sensibles et résistantes à la 9-hydroxyellipticine." Paris 6, 1986. http://www.theses.fr/1986PA066109.
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Fayet, Axel. "Détoxification d'hydolysats hémicellulosiques par dia-nanofiltration, étude de leur fermentescibilité et du mode d'action des inhibiteurs." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLA008/document.
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La biomasse lignocellulosique (BLC) est, à l’heure actuelle, la meilleure alternative au pétrole en ce qui concerne la production d’énergie et de molécules à haute valeur ajoutée. Seulement, son exploitation nécessite l’emploi de prétraitements dont les plus courants génèrent des composés inhibant la croissance des microorganismes (dérivés furaniques, acides aliphatiques, phenols).Le but de ces travaux de thèse est donc de répondre à la question suivante : “Est il possible d’utiliser la nanofiltration pour éliminer les composés inhibiteurs présents dans un hydrolysat hémicellulosique, afin de le rendre fermentescible par Bacillus subtilis 168 ?”La détermination des concentrations minimales inhibitrices de ces composés inhibiteurs sur Bacillus subtilis 168 ont permis de fixer la quantité d’inhibiteurs à éliminer de l’hydrolysat.La dia-nanofiltration à l’aide de la membrane DK (GE, USA) a permis d’éliminer de manière efficace (+ de 90%) les dérivés furaniques et les acides alphatiques. Toutefois l’émination des composés phénoliques s’est révélée plus complexe, ainsi seul 25% du syringaldéhyde a été éliminé.La cytométrie en flux a permis de montrer une action de l’acide férulique et de la vanilline sur la fluidité et la polarisation de la membrane plasmiqueLignocellulosic biomass is a promising alternative to oil for the production of energy and high added value molecules. However, its exploitation requires the use of pretreatment processes. The most commonly used processes generate by-products which present inhibitory action on microorganisms (furan derivatives, aliphatic acids, phenolic compounds).The main goal of this thesis project is to answer the following question : “Is it possible to use nanofiltration to remove inhibitory compounds from hemicellulosic hydrolysate, in order to ferment the latter with Bacillus subtilis 168 ?”Determination of minimal inhibitory concentrations of these inhibitory compounds allowed to determine, for each one, the quantity to remove from the hydrolysate.Dia-nanofiltration with DK membrane (GE, USA) allowed to efficiently remove (more than 90%) furane derivatives of aliphatic acids. However, removal of phenolic compounds was more complexe, hence, only 25% of syringaldehyde could be removed. Though most indentified inhibitory compounds were removed, Bacillus subtilis 168 was still not able to ferment the hydrolysate.Flow cytometry showed that férulic acid and vanillin presented an impact on Bacillus subtilis 168 plasma membrane fluidity of polarisation
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BEJAR, SAMIR. "Etudes de la region du terminus du chromosome d'escherichia coli k12 : replication et controle de la division cellulaire." Toulouse 3, 1986. http://www.theses.fr/1986TOU30190.
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Mousseau, Mireille. "Étude des mécanismes moléculaires de chimiorésistance intrinsèque des tumeurs cérébrales humaines." Grenoble 1, 1992. http://www.theses.fr/1992GRE10186.
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La chimiothérapie a une faible efficacité sur les tumeurs cérébrales humaines (taux de réponse objective allant de 13 a 33%). Nous avons étudié les mécanismes moléculaires de chimiorésistance intrinsèque sur une série de 66 tumeurs cérébrales humaines comportant 31 gliomes (1 gangliogliome grade 1, 9 astrocytomes grade 2 et 10 grade 3, 11 gliomes grade 4), 18 méningiomes, 12 métastases cérébrales (de 2 cancers bronchiques épidermoïdes; de 8 adénocarcinomes du sein (3 cas), du poumon (2 cas), d'origine indéterminée (2 cas) et du colon (1 cas); d'1 sarcome d'Ewing; d'1 cancer bronchique peu différencié), 1 médulloblastome, 1 tératome malin, 3 épendymomes. L'analyse en southern blot de l'ADN de 33 tumeurs cérébrales humaines, hybride avec la sonde de la résistance pléiotropique (MDR1) ne montre jamais d'amplification de ce gène. Cette résistance pléiotropique et les 3 autres mécanismes principaux de chimiorésistance ont été étudiés par la technique du northern blot avec les sondes de la résistance pléiotropique (MDR1), de la glutathion-s-transférase (GSTPIL), de la dihydrofolate réductase (DHFR) et de la topoisomérase 2 (topo 2). Le principal résultat de ce travail est la non-expression du gène de la topoisomérase 2 dans le tissu cérébral humain normal (100%) et dans 75% (44/59) des échantillons tumoraux. Le deuxième gène, GSTPI, est surexprimé dans 23% (12/53) des tumeurs cérébrales (6/32 des tumeurs cérébrales primitives, 3/10 métastases, 3/11 des méningiomes). Les deux autres gènes lies a la chimiorésistance sont trouvés exceptionnellement surexprimés 2% pour MDR1 (1 gliome grade 4 sur 61 tumeurs), 8% pour DHFR (4/49: 2 gliomes grade 2,3; 1 métastase; 1 méningiome). Nos résultats suggèrent qu'il existe une chimiorésistance intrinsèque dans les tumeurs cérébrales humaines; elle est associée à 2 mécanismes majeurs de résistance (topo 2, GSTPI) en cause avec les drogues utilisées dans le traitement de ces tumeurs.
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Gate, Laurent. "Influence du degré de méthylation de la daunosamine des anthracyclines dans l'apoptose, l'activité des topoisomérases et la modulation du phénotype de résistance multiple." Rouen, 2000. http://www.theses.fr/2000ROUES005.
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Nous avons étudié sur des cellules érythroleucémiques murines sensibles (FLC) et résistantes (DOX-RFLC) qui surexpriment la P-gp et présentent une diminution de l'expression des topoisomérases II, l'importance de la N-méthylation des anthracyclines dans la modulation de la résistance multidrogue. Ces travaux ont montré que l'augmentation de la N-méthylation de ces agents conduisait à une diminution de l'index de résistance et à une diminution des différences d'incorporation et d'extrusion de ces agents entre cellules DOX-RFLC et FLC. Il fut également observé que les trois molécules inhibaient l'activité des topoisomérases II en stabilisant le complexe clivable forme entre ces enzymes et l'ADN. L'étude de l'apoptose dans ces lignées montre qu'à des doses correspondant aux CI90, ces anthracyclines induisaient la mort des cellules sensibles et résistantes. L'expression de la protéine anti-apoptotique Bcl-2 n'était pas modifiée lors de l'induction de l'apoptose dans les différentes lignées. Par contre, l'expression de la protéine pro-apoptotique Bax était modifiée en fonction de l'anthracycline et du type cellulaire. Ces résultats indiquent donc que la méthylation du groupement amine des anthracyclines : 1) diminue leur transport par la P-gp et permet donc de surmonter la résistance associée à ce transporteur ; 2) ne modifie pas leur activité inhibitrice sur les topoisomérases II et 3) n'altère pas l'induction de l'apoptose dans les cellules sensibles et résistantes.
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Tseng, Ta-Sheng Andrew. "Phosphodiester hydrolysis and DNA cleavage with copper (II) macrocycles /." 2002. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Huang, Yan-Chen, and 黃彥程. "Study of DNA Hydrolysis by Three-Dimensional Metal Complexes Containing Triazaclyclononane." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/13022040536075978952.
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碩士淡江大學
化學學系
91
DNA hydrolysis reagents developed with synthesis metal complexes have important implications in the field of bioengineering and biomedical science. The new trinuclear metal complex which formed by 1,1,1-tris(hrdroxy methyl)ethane with 3 di-isoTACN complexed with metal ions, can act as strong Lewis acid or strong metal hydroxide group to enhance intramolecular reaction and the hydrolysis of phosphate diester. Using UV spectroscopy to confirm that 3-TACN and lanthanide and transition metal ions can form metal complexes and to determine the interaction among them under different temperature and concentration conditions. Moreover, the DNA hydrolysis ability of the two types of metals, 3-TACN ligands and metal complex are compared using agarose gel and supercoil plasmid DNA under different temperature and time conditions. In order to understand the DNA sequence selectivity, the method of polyacrylamide gel electrophoresis with labled 32P and X-ray film under different pH temperature and buffer solution is conducted. The result shows that [Mn+-3-TACN] can hydrolyze DNA; however, its reactivity is not as good as metal ions. In order to avoid the waste and pollution of heavy metal ions and to sufficiently and repetitively use the hydrolysis reagents, I try to introduce the concept of immobilization in to the experiment. Taking advantage of the physical property of poly(ethylene glycol), poly(ethylene glycol) is linked with a ligand which can hydrolyze DNA to form a new ligand and then is complexed with Co2+ metal ion complex to form a new hydrolysis reagent. The experiment result proves that the new reagent can sufficiently hydrolyze DNA and that poly(ethylene glycol) complexed with metal ions has a good hydrolysis ability. This fact suggests a factor for further research.
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Kim, Jong-Il. "The role of ATP hydrolysis in recA protein-mediated DNA strand exchange." 1993. http://catalog.hathitrust.org/api/volumes/oclc/29766146.html.
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Kuska, Michael S. "Structure and Stability of Oxygen-Linked DNA Adducts Derived from Phenolic Toxins." Thesis, 2013. http://hdl.handle.net/10214/6760.
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A significant focus of nucleic acids research is on the reactivity of electrophilic species with DNA to form addition products (adducts). Phenols are known to be able to form adducts at the C8 site of deoxyguanosine (dG). This dissertation studies the oxygen (O)-linked class of phenolic dG adducts for their hydrolytic stability as well as their structural impact on the DNA duplex. To determine the effect of C8 O-linked phenolic dG adducts on glycosidic bond stability spectrophotometric determination of hydrolysis kinetics was performed. The kinetics establish the adducts to be less stable than native dG in acid, but surprisingly stable under physiological conditions. Then to assess the modified duplex structure, a C8 O-linked phenolic dG adduct was incorporated into a DNA duplex. Thermal melting analysis establish the adduct as having a destabilizing effect on the regularly paired duplex and the conformational analysis suggests the phenolic lesion to be weakly mutagenic.NSERC
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Williams, Dominique. "Cleavage of Lipids and DNA by Metal Ions and Complexes." 2014. http://scholarworks.gsu.edu/chemistry_diss/94.
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Metal ions and complexes utilized as cleavage agents have influenced many synthetic approaches of scientists to assist in the cleavage and transformation of biomolecules. These metal-based synthetic cleavage agents have potential applications in biotechnology or as molecular therapeutic agents. Herein, we have examined Ce(IV) metal ion and complexes as acidic hydrolytic agents in lipid hydrolysis reactions (Chapter 2 and 3), and a copper(II) complex that photo-oxidizes DNA upon exposure to ultraviolet light (Chapter 4). In Chapter 2 we examined the hydrolysis of sphingomyelin vesicles by Ce(NH4)2(NO3)6 (Ce(IV)) and compared the results to twelve d- and f-block metal salts, hydrolysis of mixed lipid vesicles and mixed micelles of sphingomyelin by Ce(IV), and hydrolysis of phosphatidylcholine vesicles by Ce(IV), using either MALDI-TOF mass spectrometry or colorimetric assays. In Chapter 3, we described the study of a Ce(IV) complex based on 1,3-bis[tris(hydroxymethyl)methylamino]propane as a potential acidic hydrolytic agent of phospholipids using colorimetric assays and NMR spectroscopy. The hydrolytic agent provided markedly enhance hydrolysis at lysosomal pH (~ 4.8), but suppress hydrolysis when pH was raised to near-neutral pH (~ 7.2). This was due to the pKa values of the donor atoms of the ligand, in which the metal’s electrophilicity was reduced to a greater extent at ~ pH 7.2 compared to ~ pH 4.8. Chapter 4 describes the synthesis and study of a Cu(II) complex based on a hexaazatriphenylene derivative for photo-assisted cleavage of double-helical DNA. Scavenger and chemical assays suggested the formation of DNA damaging reactive oxygen species, hydroxyl and superoxide radicals, and hydrogen peroxide, in the photocleavage reactions. Thermal denaturation and UV-vis absorption studies suggested that the Cu(II) complex binds in a non-intercalative fashion to duplex DNA.
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Schutte, Brian Charles. "Changes in ATP hydrolysis and DNA topology resulting from the formation of recA protein-generated paranemic complexes." 1988. http://catalog.hathitrust.org/api/volumes/oclc/19903905.html.
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Thesis (Ph. D.)--University of Wisconsin--Madison, 1988.Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 187-193).
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"The Q motif is involved in DNA binding that affects ATP hydrolysis and unwinding in ChlR1 helicase." Thesis, 2016. http://hdl.handle.net/10388/ETD-2016-02-2413.
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Helicases are molecular motors that couple the energy of nucleoside triphosphate (NTP) hydrolysis to the unwinding and remodeling of structured DNA or RNA. The conversion of energy derived from NTP hydrolysis into unwinding of double-stranded nucleic acids is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI). The Q motif, consisting of an invariant glutamine (Q) residue, has been identified in some, but not all helicases. Compared with the seven well-recognized conserved helicase motifs, the role of the Q motif is not well known. Mutations in the human ChlR1 (DDX11) gene are associated with Warsaw Breakage Syndrome characterized by cellular defects in genome maintenance. ChlR1 is known to play essential roles to preserve genomic stability, particularly in sister chromatid cohesion. To examine the roles of the Q motif in the ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant wild type (WT) and mutant (Q23A) proteins were overexpressed and purified from HEK293T cells. The ChlR1-Q23A mutant abolished the helicase activity of ChlR1, and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but displayed normal ATP binding. The Q motif in FANCJ helicase, a ChlR1 homolog, regulates FANCJ’s dimerization, while our size exclusion chromatography (SEC) indicated that the ChlR1 protein functions as a monomer. A thermal shift assay revealed that ChlR1-Q23A has a similar melting point as ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have similar globular structures, although there are some subtle conformational differences between these two proteins. Taken together, our results suggest that the Q motif in ChlR1 helicase is involved in DNA binding but not in ATP binding.
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Kuan, Pu-Yun, and 管佈雲. "Kinetic & Catalytic Activity Study of Lanthanide Complex of DO2A & K21DA in Phosphate Diester & DNA Hydrolysis." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/64199364745414106462.
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碩士國立交通大學
生物科技研究所
86
Deoxyribonucleic acid (DNA) at the natural state is very stable; its half-life is over 100,000,000 years. Therefore, how to promote the DNA's hydrolysis rate becomes a challenge for many biochemists. In the beginning of this thesis, we are using macrocyclic ligand 1,7-bis(carboxymethyl) 1,4,7,10-tetraazacyclododecane (DO2A) and acid-1,7- diaza-4,10,13-trioxacyclopentadecane N,N'-Diacetic (K21DA) and lanthanide ions La(III) and Eu(III) to form complexes, and cleavage the phosphate diester(BNP-). By using diffFor the cleavage of the deoxyribonucleic acid, we used the HPLC to observe the hydrolysis of single-strand DNA primer by EuDO2A. After 5 hours, the 26 base DNA primer was completely hydrolyzed. We also used the agarose gel electrophoresis to observe the result of hydrolysis of double-strand DNA.It was found that DNA Form I (supercoiled form) decreased as the concentration of the complex increased, and DNA Form II (circular form) increased as the concentration of the complex increased. This proves that the E
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Bosgard, Brett R. "The chemistry of coupling 1,4,7-triazacyclononanane to silica and DNA : preparation and study of materials to promote phosphate ester hydrolysis and preparation of compounds to study DNA bending /." 2002. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Zhao-YiChang and 張兆毅. "para-Pyridinium Chromophore of Green Fluorescence Protein Analogue：Synthesis, Photo/Thermal Isomerization, Acidic Hydrolysis and Discussion the Mechanism of Intercalation with DNA." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/hsd7x2.
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Madeira, Catarina Alexandra Catanas. "Activity of the major autolysin of Staphylococcus aureus Atl in the presence of extracellular DNA." Master's thesis, 2018. http://hdl.handle.net/10362/53142.
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Starkuviene, Vytaute. "Identifizierung und Charakterisierung von thermostabilen Uracil Glykosylasen von Archaeon Methanobacterium thermoautotrophicum und Bakterium Thermus thermophilus." Doctoral thesis, 2001. http://hdl.handle.net/11858/00-1735-0000-0006-AC13-A.
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Lee, Crystal J. J. "Molecular Mechanisms and Determinants of Species Sensitivity in Thalidomide Teratogenesis." Thesis, 2012. http://hdl.handle.net/1807/36210.
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The expanding therapeutic use of thalidomide (TD) remains limited by its species-specific teratogenicity in humans and rabbits, but not rodents.
The R and S isomers of TD may be selectively responsible for its respective therapeutic and teratogenic effects, but rapid in vivo racemization makes this impossible to confirm. Fluorothalidomide (FTD), a fluorinated TD analogue with stable, non-racemizing isomers, may serve as a model compound for determining stereoselective effects. In vivo, FTD was undetectable in plasma, suggesting rapid breakdown, as confirmed in vitro, where FTD hydrolyzed up to 22-fold faster than TD. Unlike TD, FTD in pregnant rabbits and mice was highly toxic and lethal to both dams and fetuses. In rabbit embryo culture, FTD initiated optic (eye) vesicle and hindbrain but not classic limb bud embryopathies. Chemical instability, potent general toxicity and absence of limb bud embryopathies make FTD an unsuitable stereoselective model for TD teratogenesis.
TD teratogenesis may involve its bioactivation by embryonic prostaglandin H synthases (PHSs) to a free radical intermediate that increases embryopathic reactive oxygen species (ROS) formation. However, the teratogenic potential of rapidly formed TD hydrolysis products and the determinants of species-specific teratogenesis are unclear.
For some teratogens, mouse strains that are resistant in vivo are susceptible in embryo culture, suggesting maternal and/or placental determinants of risk. However, TD and two hydrolysis products, 2-phthalimidoglutaramic acid (PGMA) and 2-phthalimidoglutaraic acid (PGA), were non-embryopathic in CD-1 mouse embryo culture. Also, mice deficient in oxoguanine glycosylase 1 (OGG1), which repairs oxidatively damaged DNA, were resistant to TD embryopathies in culture and in vivo. Therefore, murine resistance to TD teratogenesis is dependent on embryonic factors, rather than maternal/placental determinants or increased DNA repair.
In contrast, rabbit embryos exposed in culture to TD, PGMA and PGA exhibited head/brain, otic (ear) vesicle and classic limb bud embryopathies, validating the first mammalian embryo culture model for TD teratogenesis and providing the first evidence of a teratogenic role for TD hydrolysis products. Pretreatment with eicosatetraynoic acid (ETYA), a dual PHS/lipoxygenase inhibitor, or phenylbutylnitrone (PBN), a free radical spin trapping agent, completely blocked TD, PGMA and PGA-initiated embryopathies, implicating a PHS-dependent, ROS-mediated embryopathic mechanism.
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Ward, Ian M., S. P. Hill, P. G. Klein, J. Rose, De Oca H. Montez, and D. Farrar. "Dynamic mechanical studies of hydrolytic degradation in isotropic and oriented Maxon B." 2009. http://hdl.handle.net/10454/3171.
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NoHydrolytic degradation studies have been undertaken on Maxon B, a bioresorbable block copolymer of polyglycolic acid (PGA) and polytrimethylene carbonate (TMC). Isotropic and oriented samples were studied by dynamic mechanical measurements over a wide range of temperatures. In addition to mechanical tests, water content and mass loss were also determined on the degraded samples. At early stages of degradation water content was the dominant factor and plasticisation lead to reductions in the glass transition temperatures of the PGA and TMC components. Orientation was shown to give significant improvements in the mechanical properties, including overall increases in modulus and an increase in the glass transition temperature of the PGA component, which is important for the behaviour at body temperature (37 °C). Oriented samples also showed significantly less reduction in mechanical properties on degradation. Simple one-dimensional Takayanagi models were used to provide useful insight into the understanding of the mechanical behaviour.
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陳家翎. "Kinetics studies of lanthanide polyaza polycarboxylate macrocyclic complexes Ln(DO2A) and their applications in DNA/RNA hydrolytic scission." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/47863230735046783905.
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碩士國立交通大學
生物科技研究所
88
ENGLISH ABSTRACT Since the first wholly synthetic artificial ribozyme was published in 1994, DNA and RNA whose half-life is very long can also be degradation in the short time. Therefore, it took scientists’ attention and researches, and is to promote the DNA’s or RNA’s hydrolysis rate became a challenge for many biochemists. Because the artificial restriction enzyme may be applied for gene engineering and probably provided a more effective and harmless cure. In the beginning of this thesis, we are using macrocyclic ligand 1,7-bis(carboxymethyl)1,4,7,10-tetraazacyclododecane (DO2A) and lanthanide ions to from complexes, and study their dissociation kinetics. Based on the obtained rate constants, we have found that, DO2A have strong binding affinity with lanthanide ions. Moreover, we proved that these complexes have very high stabilities again. In the other side, we use Ce(DO2A)+ and Eu(DO2A)+ to cleavage double-strand DNA(pUC19) and obtained the value of kcat are 1.0601×10-3, 3.426×10-4(s-1) and Km are 1.785×10-3,9.13210×-4(M). Further, we use Eu(DO2A)+ to hydrolysis the phosphate triester bonds at the cap structure of the mRNA. Also, we achieved the kcat which is 1.746×10-4(s-1). Compared with other’s data, it proved that the complexes have the excellent capability to cleave DNA and RNA.
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Rankin, Katherine M. "Structure and Properties of C8-Aryl-2'-Deoxyguanosine Adducts: From Mutagenic Lesions to Conformational Probes in Duplex DNA." Thesis, 2012. http://hdl.handle.net/10214/4935.
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A significant focus of toxicological research is the identification of electrophiles that covalently modify DNA to form addition products (adducts). These products can be generated when aryl radical species react at the C8-site of 2'-deoxyguanosine (dG) to form C8-aryl-dG adducts, which are mutagenic lesions. While this form of DNA modification is detrimental, C8-aryl-dG adducts also possess intriguing properties that can be exploited for beneficial purposes. This thesis is an investigation of one mechanism believed to contribute to the mutagenicity of C8-aryl-dG adducts, as well as a study of the photophysical properties of adducts that allow for their application as fluorescent probes.
A common property of C8-aryl-dG adduction is accompaniment of abasic site formation. To determine how the C8-aryl moiety contributes to sugar loss, UV-Vis spectroscopy has been employed to determine hydrolysis kinetics, with C8-aryl-dG adducts found to be more prone than dG to acid-catalyzed hydrolysis. Despite adduct reactivity in acidic media, all adducts are relatively stable at pH 7, suggesting they are unlikely intermediates of abasic site formation at physiological pH. These results have allowed for development of a new rationale for depurination observed upon C8-aryl-dG adduction within duplex DNA.
The determination of photophysical parameters of C8-heteroaryl-dG adducts reveals that these nucleosides behave as fluorophores with high fluorescence quantum yields (φfl). These adducts also exhibit emission sensitivity to their solvent environment and H-bonding interactions. C8-Heteroaryl-dG adducts were incorporated in the oligonucleotide 5'-CTCG1G2CG3CCATC, at the G1 and G3 sites, that contains the recognition sequence of the NarI Type II restriction enzyme. Hybridization of the modified NarI oligonucleotides to the complementary strand containing either the C or G nucleobase opposite the adduct allowed for characterization of duplex structures by circular dichroism (CD), UV melting temperature analysis and fluorescence spectroscopy. Results suggest that the C8-heteroaryl-dG adduct favours an anti conformation with base-paired with C, while a syn conformation is favoured when base-paired to G. Adduct conformation of bulky C8-dG adducts is believed to be correlated with their known mutagenic activity. C8-Heteroaryl-dG modified nucleosides could therefore be used as fluorescent models of these adducts to aid in elucidation of adduct-induced mutagenesis in biological systems.NSERC