The effect on DNA repair in ultraviolet-irradiated human skin fibroblasts by hydroxyurea has been examined in this study using three independent methods for measuring DNA repair: the 5-bromodeoxyuridine photolysis assay which measures DNA repair replication, chromatographic measurement of thymine-containing dimers, and measurement of specific ultraviolet-endonucleasesensitive sites in irradiated DNA. Little effect of hydroxyurea was observed at the concentration of 2 mM, which is often used to inhibit semiconservative DNA synthesis; however, 10 mM hydroxyurea resulted in marked inhibition (65-70%) of excision repair. This inhibition was accompanied by a possible doubling in the size of the repaired region. The accumulation of large numbers of single-strand breaks following ultraviolet irradiation and hydroxyurea incubation seen by other investigators was not observed with the normal skin fibroblasts used in this study. A comparison of hydroxyurea effects on the different DNA repair assays indicates inhibition of one step in DNA repair also results in varying degrees of inhibition of other steps as well.

No description available.

Ce travail a porté sur la préparation de copolymères à blocs et l’étude de leur assemblage supramoléculaire basé sur des liaisons hydrogènes entre les motifs homocomplémentaires ou hétérocomplémentaires. La stratégie de synthèse était basée sur la combinaison de la polymérisation radicalaire contrôlée de type RAFT et de la chimie supramoléculaire. Dans le chapitre 2, nous avons développé une stratégie s'appuyant sur la conception d'agents RAFT portant des groupements de type thymine / diaminopyridine (DAP) capables de générer des copolymères en étoile de type « miktoarm » bien définis. Pour élargir le champ d’application de ces agents RAFT capables d’établir des liaisons H, nous avons également étudié, dans le chapitre 3, la préparation d’agents RAFT fonctionnalisés par des motifs présentant de très hautes constantes de liaison. Le couple Hamilton / barbiturate (log (K) ≈ 4-5) a été sélectionné pour générer de plus stables copolymères à blocs supramoléculaires. Afin d’élaborer des macromolécules originales aux hautes propriétés d’association et de simplifier la stratégie de la synthèse, nous avons finalement exploré la préparation de copolymères tribloc ABC supramoléculaires à base de PA11 (oligomères OPA11) dans le chapitre 4. L’introduction d'un groupe dithiobenzoate pertinemment choisi sur les oligomères conduit à l’obtention de macroagents RAFT qui permettent la préparation de copolymères tribloc ABC supramoléculaires, où A est semi-cristallin, B à l'état caoutchouteux et C à l'état vitreux. Les études sur l'incorporation de tels copolymères dans les réseaux époxy sont en cours. / This work dealt with the preparation and the study of supramolecular block copolymers based on hydrogen-bonding between homocomplementary or heterocomplementary stickers. The synthetic strategy was based on the combination of RAFT-mediated controlled radical polymerization and supramolecular chemistry. In the Chapter 2, we developed a strategy relying on the design of RAFT agents bearing thymine/diaminopyridine (DAP) recognition pairs and capable to grow well-defined miktoarm star supramolecular copolymers. To further extend the scope of H-bonding RAFT agents, in the Chapter 3, we also investigated the preparation of RAFT agents functionalized with motifs exhibiting very high binding constants. The Hamilton/barbiturate couple (log(K)≈4-5) was selected to generate more stable supramolecular block copolymers. Aiming at elaborating original associating macromolecules and at simplifying the strategy of synthesis, we finally explored the preparation ABC triblock supramolecular copolymers based on PA11 oligomers (OPA11) in Chapter 4. Ligation of a relevant dithiobenzoate group on the oligomers afforded oligomeric RAFT agents that allow for the preparation of ABC triblock supramolecular copolymers, where A is semi-crystalline, B in rubbery state and C in glassy state. Studies on the incorporation of such copolymers in epoxy networks are under progress.

L'objectif de ce travail est de mieux comprendre le mécanisme intime de réparation de lésions photoinduites de l'ADN (dimères de type cyclobutane et adduits pyrimidine (6-4) pyrimidone) par les enzymes redox de type photolyase, en utilisant les outils et les concepts de l'électrochimie moléculaire.<br />L'étude par voltamétrie cyclique de modèles des lésions de type cyclobutane nous a permis d'une part de mimer l'étape clef de la réparation enzymatique (transfert d'électron dissociatif) et d'autre part de suivre dans le temps la réparation des lésions modèles par la photolyase ADN d'Escherichia coli. A partir des résultats obtenus, nous avons pu discuter le mécanisme de réparation, en particulier le caractère concerté ou séquentiel des réactions à l'oeuvre.<br />Le mécanisme de réparation des adduits (6-4) n'est pas encore élucidé mais une voie possible implique comme précédemment un transfert d'électron couplé à la coupure de deux liaisons vers la forme fermée des lésions (oxétanes). L'étude par voltamétrie cyclique d'une part de la réduction et de l'oxydation d'oxétanes modèles et d'autre part de leur réparation par la photolyase ADN d'E. coli nous a permis de rassembler une série de preuves expérimentales qui confirment le mécanisme initialement proposé et permettent de mieux le comprendre.

En aquesta tesi he estudiat l'efecte de l'error de superposició de base (BSSE) en la planaritat d'algunes molècules. He observat que l'ús d'alguns mètodes de càlcul amb determinades funcions de base descriuen mínims d'energia no planars per les bases nitrogenades de l'ADN. He demostrat que aquests problemes es poden arreglar utilitzant el mètode Counterpoise per corregir el BSSE en els càlculs. En aquesta tesi també he estudiat la fotofísica de la timina i els resultats mostren que existeixen dos camins de relaxació des de l'estat excitat que permeten la regeneració de l'estructura inicial de forma ultraràpida. / The effect of the basis set superposition error (BSSE) on the planarity of some molecules has been studied in this thesis. I have observed that the use of some correlated methods with certain basis sets lead to non-planar minima structures of nucleobases. I have shown that the use of the Counterpoise method fixes these pitfalls in all cases. I have also studied the photophysics of thymine in this thesis and my results show that there exist two decay paths that can regenerate the initial structure of thymine in less than tenths of picoseconds upon photon absorption.

I. Combined cloud point extraction and Tween 20-stabilized gold nanoparticles for colorimetric assay of silver nanoparticles in environmental water This study investigated a simple, sensitive and selective method for the colorimetric assay of silver nanoparticles (AgNPs) using Triton X-114-based cloud point extraction (CPE) as a preconcentration step and Tween 20-stabilized gold nanoparticles (Tween-AuNPs) as a colorimetric probe. After heating beyond the cloud point temperature of Triton X-114, a solution containing Triton X-114 micelles and AgNPs separated into a surfactant-rich phase (small volume) and a dilute aqueous phase. AgNPs partitioned into a Triton X-114-rich phase through a hydrophobic interaction between Triton X-114 micelles and AgNPs. After phase separation, the concentrated AgNPs oxidized to form Ag+ upon adding H2O2. The generated Ag+ triggered the aggregation of Tween 20-AuNPs in a high-ionic-strength solution because the reduction of Ag+ on the AuNP surface enabled Tween 20 (stabilizer) to be removed from the NP surface. The efficiency of Triton X-114-based CPE of the AgNPs was found to be iv insensitive to their size and coating type. Under optimal extraction and detection conditions, the selectivity of this method for AgNPs was considerably higher than for other nanomaterials. The minimum detectable concentrations for 7, 22, and 54 nm AgNPs were measured to be 0.1, 420, and 600 ng/mL, respectively. This method was successfully applied to the analysis of 7 nm AgNPs in drinking water, tap water and seawater. Keyword: silver nanoparticles, gold nanoparticles, cloud point extraction, Tween-20, colorimetric assay II. Functionalized silver nanoparticles as an extracting and preconcentrating agent for detection of mercury ions In this research we provided highly sensitive and selective for fluorescence assay of combined polythymine oligonucleotide (PolyT) with silver nanoparticles (AgNPs) as an extracting agent to detect mercury ion in environmental water. According to previous researches, PolyT will form a hairpin structure in the presence of Hg2+, this structure provide several 3-D grooves that the fluorescent dye can inlay with it. SYBR Green I (SG) is a staining dye for DNA, when binding with single strand DNA, it shows low fluorescence. On the contrast, SG inlay with grooves of hairpin structure, it shows v 11-fold of fluorescence signal. Hence, we used SG as a fluorescence probe for Hg2+. We modified thiol group at the 5¡¦ of PolyT DNA, because of forming silver sulfur bond, PolyT will able to modified on the surface of AgNPs. PolyT33SH-AgNPs are the extracting and concentrating agent in Hg2+ solution, by the centrifugation, we collected the PolyT33SH-AgNPs. For the purpose of releasing PolyT from AgNPs¡¦ surface, we adding H2O2 to oxidize the AgNPs into Ag+. By mixing buffer and SG into previous solution, mercury ion could be detected. In this study, we successfully detecting Hg2+ in the aqueous solution contained drinking water and tap water. The detection limit in drinking water is 20 pM, which is below Environmental Protection Agency limit for Hg2+ in drinkable water (10 nM), the linear range is from 50-600 pM. On the other hand, the detection limit in tap water is 50 pM, linear range is from 100-700 pM. Keyword: silver nanoparticles, mercury ion, PolyT, SYBR Green I, thymine

The ring opening polymerization of D,L-lactide (DLLA) using multifunctional hydroxyl-terminated initiators and catalyst/coinitiator systems based on Sn(Oct)2 afforded the preparation of star-shaped, poly(D,L-lactide)s (PDLLA)s of controlled molar mass, narrow molar mass distributions, and well-defined chain end functionality. Various modifications of star-shaped PDLLA resulted in macromolecules with tailored functionalities for biomedical applications. Star-shaped PDLLAs were modified to contain photoreactive methacrylate end groups and subsequent photo-crosslinking was performed. Photo-crosslinked networks based on methacrylated star-shaped PDLLAs exhibited thermal properties and mechanical performance that were superior to current approved clinical adhesives. In addition, the thermal and mechanical properties of the networks were strongly dependent on the composition and molar mass of the star-shaped PDLLA precursors. Tensile strengths in the range of 8-21 MPa were obtained while the Young's modulus increased from 12 to 354 MPa and were higher for networks based on urethane containing polymers. Star-shaped PDLLAs bearing complementary adenine and thymine terminal units were also prepared. The hydrogen bonding associations between complementary PDLLA macromolecules depended strongly on molar mass and hence, the concentration of multiple hydrogen bonding units. 1H NMR spectroscopy confirmed the formation of hydrogen-bonded complexes with a 1:1 optimal stoichiometry and an association constant of 84 M-1. The hydrogen-bonded complexes also exhibited significantly higher solution viscosities than non-blended polymer solutions of similar molar mass and concentration. Thermoreversible associations of PDLLA-based complementary polymers were observed in the melt phase and the melt viscosity of a blended complex was consistently an order of magnitude higher than non-functionalized star-shaped PDLLA of similar molar mass. Furthermore, melt electrospinning of the hydrogen-bonded complexes successfully resulted in fibers of significantly larger diameter (9.8 ± 2.0 µm) compared to the individual precursors (PDLLA-A = 4.0 ± 0.6 µm and PDLLA-T = 4.4 ± 1.0 µm). These results suggested that thermoreversibility, as well as the strength of the hydrogen bonding interactions between the end groups of the tailored star-shaped PDLLA-based supramolecular polymers controlled the fiber diameter in the melt electrospinning process. Highly ordered microporous honeycomb structures were developed on photo-functional star-shaped PDLLA surfaces. The pore dimensions were dependent on polymer solution concentration, polymer molar mass and relative humidity. The combination of self-organizing and cross-linking techniques resulted in free-standing, PDLLA membranes with high chemical stability as well as higher mechanical strength for further material patterning. Amikacin, an antibiotic commonly used for treating infections was successfully encapsulated in star-shaped PDLLA fibers that were electrospun from solution. Preliminary results suggested that molecular architecture influenced the encapsulation of the antibiotic and subsequent drug release profile. / Ph. D.

A oxidação do DNA por espécies reativas de oxigênio, como o oxigênio molecular singlete [O2 (1&#916;g)] , pode estar relacionada ao aparecimento de mutações e ao desenvolvimento de doenças. O O2 (1&#916;g) pode ser gerado biologicamente por reação de fotossensibilização, pela reação de H2O2 e HOCl e pela decomposição de peróxidos orgânicos contendo hidrogênio alfa (&#945;-ROOH), na presença de metais de transição (Fe2+, Cu2+) ou HOCl. A decomposição de &#945;-ROOH, como hidroperóxidos de lipídeos ou proteínas na presença de metais de transição, pode gerar O2 (1&#916;g) via mecanismo de Russell. Neste mecanismo, a oxidação de &#945; -ROOH gera radicais peroxila, que podem reagir entre si, formando um intermediário tetraóxido linear. Este intermediário tetraóxido linear pode decompor através de um mecanismo cíclico e produzir O2 (1&#916;g), um álcool e um composto carbonílico. Como a decomposição de &#945;-ROOH pelo mecanismo de Russell pode ser uma importante fonte biológica de O2 (1&#916;g) decidimos investigar se o &#945;-hidroperóxido de timina, 5-(hidroperoximetil)uracil (5-HMPU), poderia gerar esta espécie reativa na presença de metais (Ce4+, Fe2+, Cu2+) e HOCl. Outro objetivo foi avaliar os efeitos oxidativos, em DNA plasmidial (pBR322), da decomposição de 5-HPMU na presença de Cu2+. A geração de O2 (1&#916;g) na reação de 5-HPMU e Ce4+ ou HOCl foi demonstrada por meio do monitoramento da emissão de luz monomolecular de O2 (1&#916;g) na região do infravermelho próximo (IR-próximo, &#955; = 1270 nm) e bimolecular na região do visível (&#955; = 634 e 703 nm). A aquisição do espectro de emissão de O2 (1&#916;g) forneceu evidências inequívocas da geração desta espécie reativa na reação de 5-HPMU e Ce4+ ou HOCl. Além disto, a formação de O2 (1&#916;g) na reação de 5-HPMU e Fe2+, Cu2+ ou HOCl foi demonstrada através da captação química de O2 (1&#916;g) utilizando 9,10- divinilsulfonatoantraceno (AVS) e detecção por HPLC/MS/MS do endoperóxido (AVSO2) formado. A detecção por HPLC/MS/MS dos produtos de decomposição de 5-HPMU, 5- (hidroximetil)uracila (5-HMU) e 5-formiluracila (5-FoU), reforçaram a hipótese de geração de O2 (1&#916;g) pelo mecanismo de Russell. A análise dos resultados da incubação de pBR322, 5-HPMU e crescente concentração de Cu2+ mostraram o aumento da forma circular aberta (OC), indicando a formação de quebra de fita simples do DNA, provavelmente proveniente da presença dos radicais peroxila e alcoxila de 5-HPMU. Já a utilização das enzimas de reparo FPG e NTH na incubação de pBR322, 5-HPMU e Cu2+ forneceu evidências da formação preferencial de purinas oxidadas, especialmente de 2&#8217;-desoxiguanosina (dGuo). O aumento significativo da forma OC na presença de FPG indicou a formação de 8-oxo-2&#8217;-desoxiguanosina, resultante da oxidação da dGuo por O2 (1&#916;g) e/ou pelos radicais derivados de 5-HPMU. Podemos concluir que 5-HPMU pode ser uma importante fonte biológica de O2 (1&#916;g) . Além disto, a presença de 5-HPMU pode levar a propagação dos danos oxidativos no DNA, pois sua decomposição pode gerar radicais peroxila e alcoxila / Oxidation of DNA by singlet molecular oxygen O2 (1&#916;g) can be involved in the development of mutations and diseases. In vivo, O2 (1&#916;g) can be generated by photosensitization reaction, H2O2 and HOCl reaction and decomposition of organic hydroperoxides with &#945;-hydrogen (&#945;-ROOH) in the presence of metal ions (Fe2+, Cu2+) or HOCl. The &#945;-ROOH decomposition, such as lipid or protein hydroperoxides in the presence of metal ions or HOCl can generate O2 (1&#916;g) by Russell mechanism. In this mechanism, the self-reaction of peroxyl radicals generates a linear tetraoxide intermediate that decomposes to O2 (1&#916;g) , an alcohol and an aldehyde. Therefore, the purpose of this work is to investigate if O2 (1&#916;g) can be generated by &#945;-thymine hydroperoxide, 5- (hydroperoxymethyl)uracil (5-HPMU) in the presence of Ce4+, Fe2+, Cu2+ or HOCl. Another purpose is to study base modification and strand breaks formation in plasmid DNA (pBR322) by 5-HPMU decomposition in the presence of Cu2+. The generation of O2 (1&#916;g) in the reaction of 5- HPMU and Ce4+ or HOCl was monitored by monomol light emission in the near-infrared region (NIR, &#955; = 1270 nm) and dimol light emission in the visible region (&#955; = 634 e 703 nm). The generation of O2 (1&#916;g) during the reaction of 5-HPMU and Ce4+ or HOCl was confirmed by acquisition of the light emission spectrum in the NIR. Furthermore, the generation of O2 (1&#916;g) produced by 5-HPMU and Fe2+, Cu2+ or HOCl was also confirmed by chemical trapping using anthracene-9,10-divinylsulfonate (AVS) and HPLC/MS/MS detection of the corresponding endoperoxide (AVSO2). The detection by HPLC/MS/MS of 5-(hydroxymethyl)uracil (5-HMU) and 5-formyluracil (5-FoU), two 5-HPMU decomposition products, support the Russell mechanism. Plasmid results from pBR322, 5-HPMU and Cu2+ reaction showed formation of DNA open circular form (OC), probably produced by 5-HPMU peroxyl and alkoxyl radicals. Additionally, the reaction of pBR322, 5-HPMU and Cu2+ following by Fpg and NTH enzyme treatment demonstrated evidences of purine modification, especially 2&#8217;-deoxyguanosine (dGuo). The use of FPG enzyme indicated the formation of 8-oxo-7,8-dihydro-2&#8217;-deoxyguanosine, a dGuo oxidation product formed by O2 (1&#916;g) and/or 5-HPMU peroxyl and alkoxyl radicals. We can conclude that 5-HPMU can be a biological source of O2 (1&#916;g)] and 5-HPMU decomposition can lead to an enhancing of DNA oxidative damage by 5-HPMU peroxyl and alkoxyl radicals formation

A oxidação do DNA por espécies reativas de oxigênio, como o oxigênio molecular singlete [O2 (1&#916;g)] , pode estar relacionada ao aparecimento de mutações e ao desenvolvimento de doenças. O O2 (1&#916;g) pode ser gerado biologicamente por reação de fotossensibilização, pela reação de H2O2 e HOCl e pela decomposição de peróxidos orgânicos contendo hidrogênio alfa (&#945;-ROOH), na presença de metais de transição (Fe2+, Cu2+) ou HOCl. A decomposição de &#945;-ROOH, como hidroperóxidos de lipídeos ou proteínas na presença de metais de transição, pode gerar O2 (1&#916;g) via mecanismo de Russell. Neste mecanismo, a oxidação de &#945; -ROOH gera radicais peroxila, que podem reagir entre si, formando um intermediário tetraóxido linear. Este intermediário tetraóxido linear pode decompor através de um mecanismo cíclico e produzir O2 (1&#916;g), um álcool e um composto carbonílico. Como a decomposição de &#945;-ROOH pelo mecanismo de Russell pode ser uma importante fonte biológica de O2 (1&#916;g) decidimos investigar se o &#945;-hidroperóxido de timina, 5-(hidroperoximetil)uracil (5-HMPU), poderia gerar esta espécie reativa na presença de metais (Ce4+, Fe2+, Cu2+) e HOCl. Outro objetivo foi avaliar os efeitos oxidativos, em DNA plasmidial (pBR322), da decomposição de 5-HPMU na presença de Cu2+. A geração de O2 (1&#916;g) na reação de 5-HPMU e Ce4+ ou HOCl foi demonstrada por meio do monitoramento da emissão de luz monomolecular de O2 (1&#916;g) na região do infravermelho próximo (IR-próximo, &#955; = 1270 nm) e bimolecular na região do visível (&#955; = 634 e 703 nm). A aquisição do espectro de emissão de O2 (1&#916;g) forneceu evidências inequívocas da geração desta espécie reativa na reação de 5-HPMU e Ce4+ ou HOCl. Além disto, a formação de O2 (1&#916;g) na reação de 5-HPMU e Fe2+, Cu2+ ou HOCl foi demonstrada através da captação química de O2 (1&#916;g) utilizando 9,10- divinilsulfonatoantraceno (AVS) e detecção por HPLC/MS/MS do endoperóxido (AVSO2) formado. A detecção por HPLC/MS/MS dos produtos de decomposição de 5-HPMU, 5- (hidroximetil)uracila (5-HMU) e 5-formiluracila (5-FoU), reforçaram a hipótese de geração de O2 (1&#916;g) pelo mecanismo de Russell. A análise dos resultados da incubação de pBR322, 5-HPMU e crescente concentração de Cu2+ mostraram o aumento da forma circular aberta (OC), indicando a formação de quebra de fita simples do DNA, provavelmente proveniente da presença dos radicais peroxila e alcoxila de 5-HPMU. Já a utilização das enzimas de reparo FPG e NTH na incubação de pBR322, 5-HPMU e Cu2+ forneceu evidências da formação preferencial de purinas oxidadas, especialmente de 2&#8217;-desoxiguanosina (dGuo). O aumento significativo da forma OC na presença de FPG indicou a formação de 8-oxo-2&#8217;-desoxiguanosina, resultante da oxidação da dGuo por O2 (1&#916;g) e/ou pelos radicais derivados de 5-HPMU. Podemos concluir que 5-HPMU pode ser uma importante fonte biológica de O2 (1&#916;g) . Além disto, a presença de 5-HPMU pode levar a propagação dos danos oxidativos no DNA, pois sua decomposição pode gerar radicais peroxila e alcoxila / Oxidation of DNA by singlet molecular oxygen O2 (1&#916;g) can be involved in the development of mutations and diseases. In vivo, O2 (1&#916;g) can be generated by photosensitization reaction, H2O2 and HOCl reaction and decomposition of organic hydroperoxides with &#945;-hydrogen (&#945;-ROOH) in the presence of metal ions (Fe2+, Cu2+) or HOCl. The &#945;-ROOH decomposition, such as lipid or protein hydroperoxides in the presence of metal ions or HOCl can generate O2 (1&#916;g) by Russell mechanism. In this mechanism, the self-reaction of peroxyl radicals generates a linear tetraoxide intermediate that decomposes to O2 (1&#916;g) , an alcohol and an aldehyde. Therefore, the purpose of this work is to investigate if O2 (1&#916;g) can be generated by &#945;-thymine hydroperoxide, 5- (hydroperoxymethyl)uracil (5-HPMU) in the presence of Ce4+, Fe2+, Cu2+ or HOCl. Another purpose is to study base modification and strand breaks formation in plasmid DNA (pBR322) by 5-HPMU decomposition in the presence of Cu2+. The generation of O2 (1&#916;g) in the reaction of 5- HPMU and Ce4+ or HOCl was monitored by monomol light emission in the near-infrared region (NIR, &#955; = 1270 nm) and dimol light emission in the visible region (&#955; = 634 e 703 nm). The generation of O2 (1&#916;g) during the reaction of 5-HPMU and Ce4+ or HOCl was confirmed by acquisition of the light emission spectrum in the NIR. Furthermore, the generation of O2 (1&#916;g) produced by 5-HPMU and Fe2+, Cu2+ or HOCl was also confirmed by chemical trapping using anthracene-9,10-divinylsulfonate (AVS) and HPLC/MS/MS detection of the corresponding endoperoxide (AVSO2). The detection by HPLC/MS/MS of 5-(hydroxymethyl)uracil (5-HMU) and 5-formyluracil (5-FoU), two 5-HPMU decomposition products, support the Russell mechanism. Plasmid results from pBR322, 5-HPMU and Cu2+ reaction showed formation of DNA open circular form (OC), probably produced by 5-HPMU peroxyl and alkoxyl radicals. Additionally, the reaction of pBR322, 5-HPMU and Cu2+ following by Fpg and NTH enzyme treatment demonstrated evidences of purine modification, especially 2&#8217;-deoxyguanosine (dGuo). The use of FPG enzyme indicated the formation of 8-oxo-7,8-dihydro-2&#8217;-deoxyguanosine, a dGuo oxidation product formed by O2 (1&#916;g) and/or 5-HPMU peroxyl and alkoxyl radicals. We can conclude that 5-HPMU can be a biological source of O2 (1&#916;g)] and 5-HPMU decomposition can lead to an enhancing of DNA oxidative damage by 5-HPMU peroxyl and alkoxyl radicals formation

<p>Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(<em>R</em>-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.</p>