Dissertations / Theses on the topic 'DNA model'
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高銘謙 and Ming-him Ko. "A multi-agent model for DNA analysis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31222778.
Full textKo, Ming-him. "A multi-agent model for DNA analysis /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21949116.
Full textLuchetti, Andrea <1976>. "Evolution of repetitive DNA in model arthropods." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/338/.
Full textFriedrich, Tomáš. "Komprese DNA sekvencí." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2010. http://www.nusl.cz/ntk/nusl-237222.
Full textSantos, Elmer Buluran. "Biologic response to papillomavirus DNA in COPV model." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621132.
Full textArredondo, Ryan. "Properties of Graphs Used to Model DNA Recombination." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/4979.
Full textDarko, Janice. "Fluorescent Labeling of Antibiotic Resistant Bacteria Model DNA." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7600.
Full textAllegrini, Paolo. "Model for Long-range Correlations in DNA Sequences." Thesis, University of North Texas, 1996. https://digital.library.unt.edu/ark:/67531/metadc279189/.
Full textTello, Cajiao John James 1990. "The influence of the DNA conformation on the radiation-induced DNA damage probabilities = A influência da conformação do DNA nas probabilidades de dano induzido por radiações." [s.n.], 2016. http://repositorio.unicamp.br/jspui/handle/REPOSIP/305738.
Full textDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
Made available in DSpace on 2018-08-30T22:42:12Z (GMT). No. of bitstreams: 1 TelloCajiao_JohnJames_M.pdf: 2614936 bytes, checksum: e5bdfc91b42434b003cad0b5fa850afb (MD5) Previous issue date: 2016
Resumo: O objetivo deste trabalho é estudar a influência da conformação do DNA na probabilidade de dano direto produzido por partículas ionizantes. Além disso, os fundamentos mecanicísticos do modelo Linear-Quadrático são investigadas através de um modelo biofísico desenvolvido neste trabalho, baseado na TADR (Teoria da Ação Dual da Radiação). Para este fim, três modelos geométricos do material genético foram construídos. Os modelos têm resolução atomística e levam em conta ? 10^9 pares de base (bps) nas configurações A,B e Z do DNA. A partir de um único bp, os diferentes níveis organizacionais no interior do núcleo da célula foram criados por meio de transformações lineares. Em seguida, o código Monte Carlo (MC) GEANT4-DNA foi usado para simular o transporte de prótons de 0.5, 1, 5, 7 e 10 MeV assim como de partículas alfa de 2, 5, 7 e 10M eV . O número de partículas em cada caso é de tal modo que as doses absorvidas estão entre 0.5 ? 16Gy. Os três modelos foram consistentes com as dimensões das estruturas reais. Em particular, os modelos foram compatíveis com a exigência de que o diâmetro da cromatina seja de 30 nm, bem como com os volumes bp reportados em outros trabalhos. Os rendimentos tanto das quebras totais quanto das quebras duplas (TSBY e DSBY) foram obtidos para cada qualidade de radiação. Além disso, a probabilidade de impacto (SHP) definida como a razão entre o volume do DNA e o volume núcleo, foi calculada teoricamente e a partir das simulações. O modelo biofísico em conjunto com as simulações MC forneceu o número de lesões letais (N_LL) em função da dose, para prótons de 0,5 e 10 MeV, e para partículas alfa de 2 e 10 MeV . Os N_LL puderam ser divididos em aqueles criados por uma única trajetória e aqueles originados pela interacção de duas trajetórias. Concluiu-se que o TSBY é praticamente determinada pela SHP e depende fracamente da qualidade de radiação incidente. No entanto, o DSBY mostrou forte dependência tanto da conformação do DNA quanto da qualidade de radiação. Isto é devido à relação entre a capacidade de agrupamento das deposições de energia para uma radiação dada e o empacotamento do DNA. Por outro lado, a análise dos mecanismos de produção de dano, baseada na TADR e testada com o modelo biofísico desenvolvido, mostraram que os efeitos de uma única trajetória (de primeira ordem) dependem linearmente com a dose. Além disso, os efeitos inter-trajetórias seguem um comportamento quadrático com a dose, com um termo linear que influencia o mecanismo de primeira ordem. Isto significa que o comportamento linear-quadrático do N_LL com a dose, tem fundamentos mecanicistas, pelo menos, na primeira fase do dano
Abstract: The aim of this work is to study the influence of the DNA conformation on the probability of direct damage induction by ionizing particles. Also, the mechanistic grounds of the Linear-Quadratic radiobiological model are investigated through the eyes of a home-made biophysical model based on the DRAT (Dual Radiation Action Theory). To this end, three geometrical models of the genetic material were constructed. The models have atomistic resolution and account for ? 10^9 base pairs (bps) in the A-, B- and Z-DNA configurations. Starting from a single bp, the different organizational levels inside the cell nucleus were created by means of linear transformations. Next, the Monte Carlo (MC) code GEANT4-DNA was used to simulate the transport of protons of 0.5, 1, 5, 7 and 10 MeV , and alpha particles of 2, 5, 7 and 10 MeV. The number of particles in each case is such that the absorbed doses range between 0.5 Gy and 16 Gy. The three models proved to be consistent with the dimensions of the real structures. In particular, the models were compatible with the 30 nm chromatin fiber diameter requirement as well as with the bp volumes reported in other works. The Total and Double Strand Break Yields (TSBY and DSBY) were obtained for every radiation quality. Also, the Site-Hit Probability (SHP) defined as the total target to the nucleus volume ratio, was computed theoretically and from the simulations. The biophysical model in conjunction with the MC simulations furnished the number of lethal lesions (N_LL) as a function of dose, for protons of 0.5 and 10 MeV , and for alpha particles of 2 and 10 MeV . The N_LL could be split into those created by a single track and those originated by interaction of two tracks. It is concluded that the TSBY is practically determined by the SHP and depends weakly on the incident radiation quality. Nevertheless, the DSBY showed strong dependence on both the DNA conformation and the radiation quality. This is due to the interplay between the energy deposition clustering capacity of a given radiation and the DNA spatial packing. On the other hand, the analysis of the mechanisms of damage production based on the DRAT and tested with the biophysical model developed, showed that single-track (first order) effects depend linearly on the dose. Moreover, inter-track effects follows a quadratic behavior with the dose, having a linear term that influences the first order mechanism. This means that the Linear-Quadratic behavior of the N_LL with the dose, has mechanistic groundings at least at the first stage of the damage
Mestrado
Física
Mestre em Física
1370449/2014
CAPES
Lee, Kyeong Eun. "Bayesian models for DNA microarray data analysis." Diss., Texas A&M University, 2005. http://hdl.handle.net/1969.1/2465.
Full textAydogan, Bulent. "A computational atomistic model of radiation damage to DNA." [Gainesville, Fla.] : University of Florida, 2001. http://etd.fcla.edu/etd/uf/2001/anp4323/Aydogan.pdf.
Full textTitle from first page of PDF file. Document formatted into pages; contains xviii, 294 p.; also contains graphics. Vita. Includes bibliographical references (p. 284-293).
Srivastava, Alok Kumar 1967. "A model for sample stacking in microcapillary DNA electrophoresis." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/29922.
Full textIncludes bibliographical references (leaves 129-135).
Sanger's method of chain termination is the method of choice in DNA sequencing, where electrophoresis is used to separate the different sized DNA. In the past decade, microfabricated capillary devices have been developed and are increasingly used to perform DNA electrophoresis. While tremendous progress has been made in the process, sample injection has not been well understood. In an earlier study, images of sample injection obtained using video microscopy showed sharp sample stacking peak at the trailing edge of the sample plug. This thesis examines the underlying physics that explain the behavior of DNA in microcapillary electrophoresis. A developed model captures the dynamics of the major electrolytes in the system. The applied voltage and the conductivity profile determine the local electric field. The electric field drives the analyte transport. The analyte consists of DNA molecules of various fragment sizes. Since the DNA concentration is smaller than the electrolyte concentration by a few orders of magnitude, its concentration does not affect the conductivity. The major components of the sample are identified, and role during injection is investigated. Analytical studies of the electrolyte boundary dynamics and evolution and the transport of DNA are presented. The effect of the buffer, applied voltage during injection, and sample mobility on stacking are shown.
(cont.) A numerical model is implemented to quantitatively predict the stacking of DNA in microcapillary electrophoresis. The numerical model has been developed for the 1-dimensional case. The model is verified using analytical results. Results of numerical models that predict the behavior of DNA under experimental conditions are presented. The numerical model is compared with real experimental data to evaluate its predictive power. Preliminary numerical simulations have also been done for 2-dimensional geometries. A procedure has been developed for design of injector lengths to obtain a given resolution of separation in a microcapillary channel of specified length. Strategies for optimization are presented for improving the performance of the devices.
by Alok Srivastava.
Ph.D.
Snodin, Benedict E. K. "Simulating large DNA nanostructures with a coarse-grained model." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:86b2d03e-3cad-423c-8db0-3d56c65ccc20.
Full textBrun, Ludovic. "Search and Capture Model in different DNA Segregation processes." Paris 7, 2011. http://www.theses.fr/2011PA077026.
Full textEukaryotic chromosome segregation and plasmid partitioning in bacteria share an initial phase of 'search and capture' during \ growing from a localized position probe the cell to find the DNA. In higher eukaryotes, the fibers are nucleated from the mien organizing center (MTOC), in yeast from the spindle pole body and in type II plasmid prokaryotic segregation they are bound ParC complex. Schematically, polymers grow from one point and try to reach targets distributed in a confined space. Remarkably the involved fibers exhibit the same kind of dynamic. We first study a model of dynamic instability based on the idea that a cap at the tip of the fiber maintains growth. The model longitudinal interactions between the terminal tubulins of each protofilament and 'gating rescues' between neighbouring protofilaments We also build a simulation to analyze the three-component segregation system of the RI plasmids in bacteria. We test the cont filament annealing or bundling during the segregation process. The effective cost of the RI plasmids segregation process for t calculated and we concluded that this active process is a cheap way to ensure DNA segregation compare to a passive mechanic. Finally we study the search and capture phase in budding yeast. We calculate the probability of capture per microtubule and find that confinement effects such as microtubule sweeping along the nuclear membrane can lead to an efficient mechanism. By live light microscopy experiments, we show that microtubules are able to pivot at their anchorage point within the spindle pole body, which dramatically reduced the search time
Baker, John C. III. "Application of the Fisher Dimer Model to DNA Condensation." VCU Scholars Compass, 2017. http://scholarscompass.vcu.edu/etd/4791.
Full textChakraverty, Ronjon. "A yeast model of Bloom's syndrome." Thesis, Open University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264397.
Full textPostránecká, Tereza. "Porovnání metod pro konstrukci barevných DNA spektrogramů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220019.
Full textAshok, M. S. "Evaluation Of The Efficacy Of DNA Vaccines For Japanese Encephalitis In A Murine Intracerebral Japanese Encephalitis Virus Challenge Model." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/169.
Full textSrivastava, Shambhavi. "An informational-dynamical approach to characterise and model the complexity of the DNA." Thesis, University of Aberdeen, 2015. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=227605.
Full textDe, Pooter Renee. "Immunomodulatory effects following naked DNA transfer in an autoimmune model." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=31218.
Full textWe have demonstrated that DNA vaccination of an autoimmune model with a autoantigen can delay disease. The simplicity and economy of such vectors and the benefits they have for the treatment of chronic disease in contrast to more inflammatory viral vectors, support future research into their use in the treatment of autoimmune diseases.
Stubbs, Thomas Michael. "DNA methylation : a model system for the study of ageing." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275689.
Full textEntazam, A. "DNA instability and pathology in a fragile premutation mouse model." Thesis, Exeter and Plymouth Peninsula Medical School, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.700491.
Full textLatham, Tom. "De novo methyltransferases, DNA methylation and cancer : a transgenic model." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/24811.
Full textShah, Sohrab P. "Model based approaches to array CGH data analysis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2808.
Full textEntezam, Ali. "DNA instability and pathology in a fragile X premutation mouse model." Thesis, Exeter and Plymouth Peninsula Medical School, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531710.
Full textByng, Martyn Charles. "A statistical model for locating regulatory regions in novel DNA sequences." Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369119.
Full textSteele, Benjamin (Benjamin Craig). "A computational model for the isothermal assembly of tiled DNA nanostructures." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/87467.
Full textCataloged from PDF version of thesis.
Includes bibliographical references (pages 47-49).
Complex DNA nanostructures have proven difficult to assemble from starting materials. Inefficient nanostructure assembly constitutes a barrier to the widespread use of DNA nanotechnology and is difficult to investigate experimentally due to the complicated nature of the assembly. This work introduces a type of tile assembly model, the isothermal tile assembly model (iTAM). The iTAM seeks to capture the behavior of assembling DNA tile nanostructures to identify design factors and reaction conditions which improve assembly yields. Simulations using the iTAM model explain the experimental observation that only a narrow range of temperatures permit optimal isothermal assembly of tile-based DNA nanostructures. This narrow temperature range reflects a balance between the stabilization of non-designed interactions at low temperatures and the destabilization of the overall designed structure at high temperature. Simulations based on the iTAM are effective at estimating the temperature of optimal assembly unique to 25 two-dimensional tile designs, with an mean error of estimation of 4.6 degrees C. Results from the iTAM indicate that optimal assembly temperatures are determined largely by the strength of tile-tile domain interactions. For a given tile design, tile concentration and the length of time represent convenient axes of control over tile assembly. Kinetic trapping that blocks complete assembly of a tile design is likely to be overcome by increasing the both temperature and tile concentration in the assembly reaction. Such a change also substantially decreases the computationally predicted time required for complete assembly.
by Benjamin Steele.
S.M.
Lapato, Dana. "Latent Growth Model Approach to Characterize Maternal Prenatal DNA Methylation Trajectories." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/5995.
Full textKhatib, Maha. "The generalized Poland-Scheraga model : bivariate renewal approach to DNA denaturation." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC293/document.
Full textThe Poland-Scheraga (PS) model is the standard basic model to study the denaturation transition of two complementary and equally long strands of DNA. This model has enjoyed a remarkable attention because it is exactly solvable in its homogeneous version. The solvable character is related to the fact that the homogeneous PS model can be mapped to a discrete renewal process. In the bio-physical literature a generalization of the model, allowing different length and non complementarity of the strands, has been considered and the solvable character extends to this substantial generalization. In this thesis we present a generalized version of the PS model that allows mismatches and non complementary strands (in particular, the two strands may be of different lengths). We consider first the homogeneous model and we exploit that this model can be mapped to a bivariate renewal process. The distribution K(⋅) of the location (in two dimensions) of the first contact between the two strands is assumed to be of the form K(n + m) = (n + m)−α−2L(n + m) with α ≥ 0 and L(⋅) slowly varying and corresponds to a loop with n bases in the first strand and m in the second. We study the localization-delocalization transition and we prove the existence of transitions inside the localized regime. We then present precise estimates on the path properties of the model. We then study the disordered version of the model by including a sequence of inde- pendent and identically distributed random variables with two indices. We focus on the influence of disorder on the denaturation transition: we want to determine whether the presence of randomness modifies the critical properties of the system with respect to the homogeneous case. We prove that the disorder is irrelevant if α < 1. We show also that for α > 1, the quenched and annealed critical points differ (basing on coarse graining techniques and fractional moment method), proving the presence of a relevant disorder regime
Zabarmawi, Yusra. "Ionizing Model to Predict the Clustered in Nucleotide Damageafter Low & High LET Radiation." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1563274274747153.
Full textDannenberg, Frits Gerrit Willem. "Modelling and verification for DNA nanotechnology." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:a0b5343b-dcee-44ff-964b-bdf5a6f8a819.
Full textAngeleska, Angela. "Combinatorial models for DNA rearrangements in ciliates." [Tampa, Fla] : University of South Florida, 2009. http://purl.fcla.edu/usf/dc/et/SFE0002998.
Full textTaslim, Cenny. "Algorithm for comparing large scale protein-DNA interaction data." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306894920.
Full textDražková, Jana. "Emergentní vlastnosti sítě G1/S." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2010. http://www.nusl.cz/ntk/nusl-229035.
Full textChristopher, Andrea. "Mathematical model of 'on-demand' histone protein synthesis during S phase in humans." Thesis, University of Aberdeen, 2016. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=230770.
Full textCallow, Philip Austin. "Cationic lipid : DNA complexes - their structure and interactions with model cell membranes." Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400591.
Full textPaschalis, Vasileios. "Revised model for the DNA replication fork in Bacillus subtilis : polymerase asymmetry." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/40887/.
Full textFraga, Timiraos Ana Belén. "Model Studies on the Photorepair of (6-4) Dimeric Lesions of DNA." Doctoral thesis, Universitat Politècnica de València, 2019. http://hdl.handle.net/10251/117610.
Full text[CAT] La radiació ultravioleta està associada a la formació de certes lesions en l'ADN que podrien concluir al càncer de pell. Entre les més rellevants es troben els danys que es produïxen en les bases pirimidínicas: els dímers ciclobutánics (CPDs) i els fotopro-ductes (6-4) (6-4PPs) . Per a protegir-se de les fotolesions al l'ADN, els organismes vius disposen d'enzims que restauren les lesions a la seua forma original, mantenint així la integritat genètica. En alguns organismes els CPDs i els 6-4PPs manifesten un procés de reparació addicional, que correspon a la fotorreactivació on están involu-crats enzims denominades fotoliases CPD i (6-4) . En concret, actualment hi ha una viva discussió sobre el mecanisme de reparació per la fotoliasa (6-4) . L'objectiv gene-ral d'esta tesi doctoral ha sigut estudiar la ciclorreversió dels intermedis clau proposats per a la lesió 6-4PP com a recolzament d' un dels mecanismes proposats fins ara. En primer lloc s'ha preparat un model de l'azetidina intermèdia de la lesió 6-4PP en seqüències TC per a investigar la seua reparació per mitjà d'un procés de donació d'electrons per fotosensibilizadors amb un potencial redox adequat, mimetitzant així el cofactor flavina de la fotoliasa (6-4) . Els estudis d'electroquímica, espectroscòpia, anàlisi cromatogràfica i química computacional van mostrar que la possibilitat d'injec-tar un electró a l'anell de l'azetidina comporta una ciclorreversió de l'azetidina bipiri-midínica a les bases de timina i 6-azauracil. També s'ha evidenciat que la transferència d'electrons només té lloc si la base timina està present en el model. En segon lloc, s'ha investigat la ciclorreversión de l'azetidina mitjacant procés oxidatiu en que l'anell d'azetidina dóna un electró cap al fotosensibilizador. La compa-ració amb un derivat ciclobutánic va mostrar que la presència del nitrògen en el anell de quatre membres disminuïx el potencial redox facilitant el procés d'oxidació. En tercer lloc, el pas de ciclorreversió s'ha estudiat amb dos fotosensibilizadors intrínsecs, guanina i el dany oxidatiu 8-oxoguanina (OG) , units covalentment a un CPD o a un oxetano, com a intermedi del dany (6-4) . En conjunt, les dades d'espec-troscòpia i anàlisi cromatogràfica van mostrar la possibilitat que estos fotosensibiliza-dors endògens poden actuar com a donadors d'electrons mimetitzant, per tant, la fun-ció del cofactor flavina en la fotoliasa. Finalment, l'anell d'azetidina ha sigut incorporat en un oligonucleotid per a estu-diar la seua ciclorreversió per mitjà de una transferència electrònica. Basant-se en els resultats dels capítols previs, OG ha sigut triat com un fotorreductor natural. En un primer pas, una metodologia ha sigut desenvolupada per a inserir l'azetidina dins d'una seqüència d'oligonucleòtid. Després, la irradiació en estat estacionari del dúplex que conté OG i l'azetidina ha demostrat que la transferència d'electrons té lloc i comporta a la ciclorreversió de l'heterocicle. A més, experiments preliminars han sigut duts a terme per a avaluar la reparació de l'anell de quatre membres, com un anàleg del in-termedi en la reparació del fotoproducte (6-4) , per les fotoliases reals CPD i (6-4).
[EN] Ultraviolet radiation is associated with the formation of certain lesions in the DNA that are at the origin of skin cancer. Among the most relevant are the damages that occur at pyrimidine bases: cyclobutane dimers (CPDs) and (6-4) photoproducts (6-4) (6-4PPs). To obtain protection from DNA photolesions, living organisms have enzymes that restore the lesions to their original form, thus maintaining genetic integ-rity. In some organisms, CPDs and 6-4PPs show an additional repair process, which corresponds to photoreactivation and involves enzymes called CPD and (6-4) photol-yases. In particular, there is currently a lively discussion about the mechanism of repair by (6-4) photolyase. The general objective of this doctoral thesis has been to study the cycloreversion of the proposed intermediate of 6-4PP lesions as a key to support one of the mechanisms proposed so far. In a first place, a model of the intermediate azetidine of the 6-4PP lesion for TC sequences was prepared to investigate its repair by means of electron donation by photosensitizers with suitable redox potential, mimicking the flavin cofactor of the (6-4) photolyase. Electrochemical, spectroscopic, analytical measurements as well as computational studies showed that the injection of an electron into the azetidine ring leads to a cycloreversion of the bipyrimidine azetidine to the thymine and 6-azauracil bases. It has also been shown that electron transfer only takes place if the thymine component is present in the model. Secondly, the cycloreversion of azetidine has been investigated by means of an oxidative process in which the azetidine ring donates an electron to the photosensitiz-er. The comparison with a cyclobutane derivative showed that the presence of the nitrogen in the four-membered ring decreases the redox potential, facilitating thus the oxidation process. Third, the cycloversion step has been studied with two intrinsic photosensitizers, guanine and the oxidatively generated damage 8-oxoguanine (OG), covalently bound to a CPD or to an oxetane, as a model for the intermediate of 6-4PP repair. Altogeth-er, the spectroscopic and analytical data showed that these endogenous photosensitiz-ers can act as electron donors mimicking, thus, the function of the flavin cofactor in photolyase. Finally, azetidine ring has been incorporated in an oligonucleotide to study its cy-cloreversion by electron transfer. Based on the results of the previous chapter, OG has been chosen as a natural photoreductant. In a first step, a methodology has been developed to insert the azetidine within the oligonucleotide sequence. Then, steady-state irradiation of the duplex containing OG and the azetidine has demonstrated that the electron transfer takes place and leads to the cycloreversion of the heterocycle. In addition, preliminary experiments have been carried out to evaluate the repair of this four-membered ring, as an analog to the (6-4) photoproduct intermediate, by real CPD and (6-4) photolyases.
Fraga Timiraos, AB. (2019). Model Studies on the Photorepair of (6-4) Dimeric Lesions of DNA [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/117610
TESIS
Peters, David G. "Characterisation of GATA binding proteins using Aspergillus nidulans as a model organism." Thesis, University of Liverpool, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240865.
Full textFalcon, Alaric Antonio. "Building an episomal model of aging in saccharomyces cerevesiae." [Gainesville, Fla.] : University of Florida, 2004. http://wwwlib.umi.com/cr/ufl/fullcit?p3136937.
Full textTypescript. Title from title page of source document. Document formatted into pages; contains 117 pages. Includes Vita. Includes bibliographical references.
Chambers, Mark Andrew. "Studies of the immune response to human papillomavirus type-16 proteins in a mouse model." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308297.
Full textBrümmer, Anneke. "Mathematical modelling of DNA replication." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2010. http://dx.doi.org/10.18452/16212.
Full textBefore a cell divides it has to duplicate its entire genetic material. Eukaryotic genomes are replicated from multiple replication origins across the genome. This work is focused on the quantitative analysis of the underlying molecular mechanism that allows these origins to initiate DNA replication almost simultaneously and exactly once per cell cycle. Based on a vast amount of experimental findings, a molecular regulatory network is constructed that describes the assembly of the molecules at the replication origins that finally form complete replication complexes. Using mass–action kinetics, the molecular reactions are translated into a system of differential equations. To parameterize the mathematical model, the initial protein concentrations are taken from experimental data, while kinetic parameter sets are determined using an optimization approach, in particular a minimization of the duration, in which a minimum number of replication complexes has formed. The model identifies a conflict between the rapid initiation of replication origins and the efficient inhibition of DNA rereplication. Analyses of the model suggest that a time delay before the initiation of DNA replication provided by the multiple phosphorylations of the proteins Sic1 and Sld2 by cyclin-dependent kinases in G1 and S phase, G1-Cdk and S-Cdk, respectively, may be essential to solve this conflict. In particular, multisite phosphorylation of Sld2 by S-Cdk creates a time delay that is robust to changes in the S-Cdk activation kinetics and additionally allows the near-simultaneous activation of multiple replication origins. The calculated distribution of the assembly times of replication complexes, that is also the distribution of origin activation times, is then used to simulate the consequences of certain mutations in the assembly process on the copying of the genetic material in S phase of the cell cycle.
Huang, Chao-Min. "Robust Design Framework for Automating Multi-component DNA Origami Structures with Experimental and MD coarse-grained Model Validation." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu159051496861178.
Full textFrith, Richard William. "Model studies relating to the mode of action of O'6-alkylguanine-DNA alkyltransferase." Thesis, University of Newcastle Upon Tyne, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285689.
Full textBellamy, Michael Bruce. "A double strand DNA break model of photon and electron relative biological effectiveness." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47711.
Full textBusch, Marc Gregory. "Evaluation of different SIV plasmid DNA vaccines : a model for HIV vaccine development /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2004. http://uclibs.org/PID/11984.
Full textSiu, Kim-Man. "A computational estimation of errors in model genomes using exactly duplicated DNA sequences /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?MATH%202005%20SIU.
Full textSilva, Eduardo Ferreira da. "Estudo da interação DNA-HOESCHT (33258) por pinçamento ótico." Universidade Federal de Viçosa, 2013. http://locus.ufv.br/handle/123456789/4267.
Full textCoordenação de Aperfeiçoamento de Pessoal de Nível Superior
By performing single molecule stretching experiments with optical tweezers, we have stu- died the DNA interaction with the ligand Hoechst(33258). The mechanical properties of the complexes as a function of ligand concentration were directly determined from these measure- ments by fitting the force versus extension curve to the WormLike Chain model of semiflexible polymers. In addition, the physico-chemical parameters of the interaction were extracted from the persistence length data by using a previously developed two-sites quenched disorder sta- tistical model, allowing the determination of the binding isotherm. This model has allowed us to decouple the two different binding modes present in this system. In particular, it was found that the binding isotherm consists of two Hill-type processes, one non-cooperative and the other strongly cooperative. Finally, DNA condensation due to the interaction with the ligand was also verified and characterized here by analyzing the apparent contour length of the complexes.
Neste trabalho, fizemos experimentos de estiramentos em moléculas únicas com pinça ótica e estudamos a interação do DNA com o ligante Hoechst(33258). As propriedades mecânicas dos complexos formados como uma função da concentracao do ligante, foram diretamente determinadas a partir destas medidas, por ajuste das curvas de forca por extensão pelo modelo da cadeia vermiforme (WLC), de polímeros semiflexíveis. Além disso, os parâmetros físico-químicos da interação foram extraídos dos dados do comprimento de persistência usando um modelo estatístico de desordem de dois sítios previamente desenvolvido, permitindo a obtenção da isoterma de ligação. A aplicação do modelo nos permitiu decompor os dois modos de ligação presentes neste sistema. Em particular, encontramos que a isoterma de ligação consiste de dois processos tipo Hill, um não cooperativo e o outro fortemente cooperativo. Finalmente a condensação do DNA devido a interação com o ligante foi também verificada e caracterizada aqui por análise do comprimento de contorno aparente do complexo.
Rachamadugu, Sairaj. "Manipulation of 3D knotted polygons." TopSCHOLAR®, 2012. http://digitalcommons.wku.edu/theses/1162.
Full textBagci, V. M. Kemal. "Anderson Localization in Two-Channel Wires with Correlated Disorder: DNA as an Application." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc5204/.
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