An overexposure to ultraviolet radiation can cause sunburn and some forms of skin cancer. UV light causes many different photoproducts. The cys-syn cyclobutylpyrimidine dimer (CPD) is the major photoproduct upon UV irradiation. DNA photolyase (PL) is a light-driven flavoprotein that repairs CPD in UV-damaged DNA. This repair process occurs in the presence of blue light through ultrafast photo-induced electron transfer from reduced anionic flavin adenine dinucleotide (FADH¯) to the CPD by an unknown mechanism. Since the excited state flavin transfers an electron to repair the damaged DNA, it is of utmost importance that we understand better the excited state properties of the flavins. In this work the excited state electronic properties of all three-oxidation states of flavin: oxidized form (FAD), semiquinone radical form (FADH•) and reduced anionic form (FADH¯) were studied using Stark spectroscopy and complimented by time dependent density functional theory (TD-DFT) calculations. These results are presented and discussed in Chapter 3 and 4. The difference dipole moments (Δμ) and the difference polarizabilities (Tr(Δα01)) were experimentally determined for first two lowest optically accessible states. The results are discussed in the context of photoreduction of flavins in wider class of flavoprotein blue light photoreceptors and catalytic electron transfer process in DNA repair. In the later part of this thesis (Chapters 5 and 6) the excited state electronic properties of monomeric 2-Aminopurine (2AP), 8-Vinyladenine 8VA were presented. These 8VA, 2AP are examples of fluorescent nucleotide analogues of adenine that can be incorporated into DNA with little perturbation of the normal double-helical structure. The fluorescence of these analogues is quenched when incorporated in double-stranded DNA (dsDNA). The basic mechanism underlying the fluorescence quenching by base stacking of 2AP and 8VA are is not well understood, and thus exploring the excited state electronic structures of these bases is an important first step. We have explored the excited state properties of 2AP and 8VA in frozen LiCl and ethanol solutions using Stark spectroscopy. High-level ab initio and TD-DFT calculations were performed to compliment the experimental results. / Chemistry

Bio-inspired monomers functionalized with nucleobase or ionic group allowed synthesis of supramolecular polymers using free radical polymerization and controlled radical polymerization techniques. Comprehensive investigations for the structure-property-morphology relationships of these supramolecular polymers elucidated the effect of noncovalent interactions on polymer physical properties and self-assembly behaviors. Reverse addition-fragmentation chain transfer (RAFT) polymerization afforded acrylic ABC and ABA triblock copolymers with nucleobase-functionalized external blocks and a low-Tg central block. The hard-soft-hard triblock polymer architecture drove microphase-separation into a physically crosslinked hard phase in a low Tg matrix. Hydrogen bonding in the hard phase enhanced the mechanical strength and maintained processability of microphase-separated copolymers for thermoplastics and elastomers. A thermodynamically favored one-to-one stoichiometry of adenine and thymine yielded the optimal thermomechanical performance. Intermolecular hydrogen bonding of two thymine units and one adenine unit allowed the formation of base triplets and directed self-assembly of ABC triblock copolymers into remarkably well-defined lamellae with long-range ordering. Acetyl protected cytosine and guanine-containing random copolymers exhibited tunable cohesive strength and peel strength as pressure sensitive adhesives. Post-functionalization converted unprotected cytosine pendent groups in acrylic random copolymers to ureido-cytosine units that formed quadruple self-hydrogen bonding. Ureido-cytosine containing random copolymers self-assembled into nano-fibrillar hard domains in a soft acrylic matrix, and exhibited enhanced cohesive strength, wide service temperature window, and low moisture uptake as soft adhesives. A library of styrenic DABCO salt-containing monomers allowed the synthesis of random ionomers with two quaternized nitrogen cations on each ionic pendant group. Thermomechanical, morphological, and rheological analyses revealed that doubly-charged DABCO salts formed stronger ionic association and promoted more well-defined microphase-separation compared to singly-charged analogs with the same charge density. Bulkier counterions led to enhanced thermal stability, increased phase-mixing, and reduced water uptake for DABCO salt-containing copolymers, while alkyl substituent lengths only significantly affected water uptake of DABCO salt-containing copolymers. Step growth polymerization of plant oil-based AB monomer and diamines enabled the synthesis of unprecedented isocyanate-free poly(amide hydroxyurethane)s, the first examples of film-forming, linear isocyanate-free polyurethanes with mechanical integrity and processability. Successful electrospinning of segmented PAHUs afforded randomly orientated, semicrystalline fibers that formed stretchable, free-standing fiber mats with superior cell adhesion and biocompatibility. / Ph. D.

The dynamic characteristics of hydrogen and ionic bonding contributes to the reversible properties of acrylic polymers, opening new avenues for designing materials with mechanical strength and processability. These non-covalent interactions function as physical crosslinks, which provide enhanced structural and mechanical integrity to acrylic block copolymers. The strong hydrogen bonding or ionic interaction also directs self-assembly to hierarchical microstructures, which enables many applications including thermoplastic elastomers and energy storage devices. Inspired by complementary hydrogen bonding interactions between nucleobase pairs in DNA, a series of bioinspired nucleobase-acrylate monomers such as adenine acrylate (AdA), thymine acrylate (ThA), cytosine acrylate (CyA) were designed, whose synthesis were afforded by aza-Michael addition. Among those nucleobases, cytosine arises as a unique category. It is not only able to self-associate via weak hydrogen bonds, but also forms quadruple hydrogen-bond bearing units (ureido-cytosine) when functionalized with isocyanates. Reversible addition-fragmentation chain transfer polymerization (RAFT) yielded acrylic ABA triblock copolymers with CyA external hard blocks. A subsequent post-functionalization using hexyl-isocyanate generated the corresponding ureido-cytosine acrylate(UCyA)-containing triblock copolymers. The self-complementary quadruple hydrogen bonding in the UCyA polymers achieved a broader service temperature window, while the alkyl chain ends of UCyA units allowed tunability of the mechanical strength to apply as thermoplastic elastomers. In addition, quadruple hydrogen bonding induced stronger propensity of self-assembly and denser packing of the polymers, which contributed to a well-defined ordered morphology and enhanced resistance to moisture uptake. A facile 2-step synthesis provided doubly-charged styrenic DABCO salt monomer(VBDC₁₈BrCl) containing an octadecyl tail. RAFT polymerization allowed the preparation of DABCO ABA block copolymers with defined molecular weights and low polydispersity. Thermal analysis revealed a melting transition of the VBDC₁₈BrCl block copolymer resulting from the side-chain crystallization of the long alkyl tail. Systematic mechanical comparisons between DABCO salt-containing copolymers and the corresponding singly-charged polymer controls demonstrated superior mechanical properties attributable to a stronger ionic interaction between the doubly-charged groups. Morphological characterizations revealed a well-ordered lamellar microstructure and a unique three-phase morphology of the DABCO block copolymers, which involve a soft phase, a hard phase, and an ionic aggregates domain dispersed within the hard domain. / Master of Science

Yes / The synthesis and self-assembly of thymine-containing polymers were performed using RAFT dispersion polymerization. A combination of microscopy and scattering techniques was used to analyze the resultant complex morphologies. The primary observation from this study is that the obtained aggregates induced during the polymerization were well-defined despite the constituent copolymers possessing broad dispersities. Moreover, a variety of parameters, including the choice of polymerization solvent, the degree of polymerization of both blocks and the presence of an adenine-containing mediator, were observed to affect the resultant size and shape of the assembly. / University of Warwick, National Science Foundation (U.S.) (NSF), Engineering and Physical Sciences Research Council (EPSRC)

Les triarylamines sont de petites molécules largement utilisées comme porteurs de charges dans le domaine de l'électronique organique, car elles présentent des mobilités de transport de trous élevées. En 2010, notre groupe a démontré pour la première fois que les molécules de triarylamine décorées avec des groupements amide subissent une polymérisation supramoléculaire. D'autre part, les propriétés de reconnaissance des résidus de nucléobases ont été largement utilisées au cours des 25 dernières années pour déclencher des processus d'auto-assemblage de polymères ou de petites molécules en polymères supramoléculaires bien définis. Dans cette thèse, une série de molécules triarylamine décorées avec des amides sur leurs chaînes latérales avec différentes nucléobases comme la guanine, la thymine et la cytosine ont été synthétisées. Nous avons démontré que les monomères de triarylamine conservent leurs propriétés d'auto-assemblage dans les solvants chlorés lors de l'irradiation lumineuse, à condition que le résidu de la nucléobase n'affecte pas les interactions non covalentes nécessaires pour l'auto-assemblage du cœur de triarylamine. En outre, nous avons démontré que la présence d'amines primaires sur le résidu de la nucléobase interdit la formation de structures auto-assemblées dès qu'elles ne sont pas incorporées dans des réseaux de liaisons hydrogène. Dans un deuxième chapitre, nous avons ensuite étudié les auto-assemblages de nos molécules triarylamine-nucléobase dans des solvants organiques en utilisant des ions ou de petites molécules comme matrice. Tout d'abord, la polymérisation supramoléculaire de la triarylamine-monothymine à l'aide de mélamine dans divers solvants a été étudiée. Par ailleurs, l'influence sélective des ions de mercure sur les propriétés sensibles légères de triarylamine-monothymine a été soigneusement analysé. Enfin, les polymères supramoléculaires hybrides de triarylamine-monoguanine conjugué en absence et en présence d'ions potassium ont été obtenus. En particulier, nous avons décrit le premier exemple de polymères supramoléculaires construits à partir de mélamine dans des solvants organiques. Dans l'ensemble, l'impact de ce travail est triple: a) il conduit à une meilleure compréhension du comportement d'auto-assemblage des conjugués de triarylamine, b) il influence la conception des structures de triarylamine auto-assemblées et c) il offre de nouvelles approches pour l'auto-assemblage des molécules de triarylamine. / Triarylamines are small molecules widely used as charge carriers in the field of organic electronics as they display high hole-transport mobilities. In 2010, our group demonstrated for the first time that chemically-tailored triarylamine amide molecules undergo supramolecular polymerization. On the other hand, the recognition properties of nucleobase residues have been widely used in the last 25 years to trigger self-assembling processes of polymers or small molecules into well-defined supramolecular polymers.In this thesis, a series of triarylamine amide molecules decorated on their side chains with various nucleobases such as guanine, thymine and cytosine have been synthesized. We have demonstrated that the triarylamine monomers retain their self-assembling properties in chlorinated solvent upon light irradiation, provided that the nucleobase residue does not affect the non-covalent interactions necessary for the self-assembly of the triarylamine core. In addition, we have demonstrated that the presence of primary amines on the nucleobase residue prohibit the formation of self-assembled structures, as soon as they are not embedded in hydrogen bonding arrays. In a second chapter, the templated self-assemblies of our triarylamine-nucleobase molecules in organic solvents were studied. Firstly, templated supramolecular polymerization of triarylamine-monothymine using melamine in various solvents was investigated. Besides, selective influence of mercury ion on the light responsive properties of triarylamine-monothymine was analyzed carefully. At last, hybrid supramolecular polymers of triarylamine-monoguanine conjugate in absence and in presence of potassium ion were obtained. In particular, we have described the first example of supramolecular polymers build from melamine in organic solvents. Overall, the impact of this work is three-fold: a) it leads to a better understanding of the self-assembly behavior of triarylamine conjugates, b) it influences the design of self-assembling triarylamine structures and c) it offers new approaches for the self-assembly of triarylamine molecules.

Cette thèse porte sur l’étude de la radio-sensibilité de Molécules AromatiquesHétérocycliques (MAH) à basse température exposées à une irradiation avec des ionslourds rapides. La présence de ces molécules dans les météorites carbonées sur Terre estune forte indication pour l’existence de cette catégorie de molécules dans l’espace.L’objectif de ce travail est de simuler l’effet des rayons cosmiques sur des MAH enphase solide et d’estimer leur résistance à l’irradiation. Les lignes de faisceaux deGANIL et de GSI permettent de simuler cet effet. L’évolution des MAH en phase solidea été monitorée par spectroscopie infrarouge à transformée de Fourier. Cela permet dequantifier la destruction des MAH, de déterminer leur section efficace de destruction etde détecter les molécules produites. Les sections efficaces de destruction de l’adénine etde la cytosine suivent une loi puissance en fonction du pouvoir d’arrêt électronique :σd~ Se1.2. Les nouvelles bandes d’absorption observées après l’irradiation des MAH sontprincipalement attribuées à des nitriles (R-C≡N), des isonitriles (R-N≡C) et (R-C≡C).L’évolution de la section efficace en fonction du pouvoir d’arrêt électronique a permisd’estimer la durée de vie de l’adénine dans l’espace : (14×106) années. Ces résultatspermettront de comprendre la stabilité et la chimie de ces molécules complexes dansl’espace. / The thesis concerns the study of the radio sensitivity of aromatic heterocyclic molecules(AHMs) at low temperature (12 K) exposed to swift heavy ion radiation. The presenceof aromatic heterocyclic molecules in carbonaceous meteorites on Earth is a strongindication that this class of molecules exists in outer space.The aim of this work was to study the effects of cosmic ray analogues on solid AHMsand to estimate their survival under radiation. The beam lines of GANIL and GSI allowto simulate the effects of cosmic rays in AHMs. The evolution of the solid AHMs underirradiation was monitored by Fourier transformed infrared absorption spectroscopy; thisallows to quantify the disappearance of AHMs, to determine their apparent destructioncross section and to detect their radioproducts. Furthermore, it was found that adenineand cytosine destruction cross sections (σd) follow a power law with the electronicenergy loss: σd~ Se1.2 .New IR absorption peaks arising from the AHMs degradationswere observed; these peaks can be attributed to nitriles (R-C≡N), isonitriles (R-N≡C),and (R-C≡C).The observed power law allowed the estimation of the lifetime of adeninein space exposed to galactic cosmic rays as (14×106) years. These findings may help tounderstand the stability and chemistry related to complex organic molecules in space.

This PhD thesis reports the development of novel C-H activation strategies and aqueous-phase Suzuki-Miyaura cross-coupling reactions for the synthesis of modified deazapurine nucleobases. The methodologies of chemo- and regioselective synthesis of highly functionalized deazapurines have been developed by using modern C-H activation chemistry. Various functional groups such as amino-, imido-, silyl- and phosphonyl- were introduced by C-H activation reactions. Amino deazapurine derivatives were synthesized by developed Pd/Cu-catalyzed direct C-H amination and C-H chloroamination of 6-substituted 7-deazapurines with N-chloro-N- alkyl-arylsulfonamides. C-H imidation reactions of pyrrolopirimidines were performed under ferrocene catalysis with N-succinimido- or N-phtalimidoperesters. In order to obtain silylated derivatives, Ir-catalyzed C-H silylations of phenyldeazapurines with alkyl silanes were designed. Highly interesting deazapurine phosphonates were prepared by using Mn-promoted C-H phosphonation method and were further transformed into the corresponding phosphonic acids. All of the developed direct C-H functionalization reactions proceeded regioselectively at position 8 in deazapurine core, except for C-H silylation where reaction undergoes mainly as directed ortho C-H silylation on phenyl ring,...

Photoinduced electron transfer (PET) plays a crucial role in a wide array of biological pathways. These electron transfer reactions happen from or to the excited state of a chromophore upon absorption of light. Hence understanding the properties of excited states is necessary in elucidating the details of such pathways. The work presented in this thesis deals with PET in two systems: Fluorescent Nucleobase Analogues (FBAs) and DNA photolyase. The introductory chapter (Chapter 1) presents some background information about the two systems and sets up the stage for the reasoning behind the problems addressed in this thesis. FBAs are fluorescent analogues of naturally occurring, weakly fluorescent native nucleic acid bases. When incorporated into single stranded (ss) or double stranded (ds) DNA, the FBA fluorescence is significantly quenched. PET has been implicated to be the cause for the observed quenching. Here we have presented our attempt to correlate the quenching behavior of free FBA: nucleic acid monophosphate (NMP) pairs with the free energies associated with excited state electron transfer delta GET. Based on the delta GET values, we have tried to assign the direction of electron transfer. The quenching behavior of the FBA:NMP pairs were studied through Stern-Volmer (SV) quenching and time-resolved fluorescence studies. The above described analysis has been applied on FBAs: 4-amino-6-methyl-8-(2'-deoxy-beta-D-ribofuranosyl)-7(8H)-pteridone (6MAP), 4-amino - 2, 6 - dimethyl - 8 - (2'-deoxy-beta-d-ribofuranosyl) -7(8H) - pteridone (DMAP), 3-methyl-8-(2'-deoxy-beta-D-ribofuranosyl) isoxanthopterin (3MI) and 6-Methyl-8-(2'-deoxy-β-D-ribofuranosyl) isoxanthopterin (6MI) (Chapter 3), 2-Aminopurine (2AP) (Chapter 4), 8-Vinyl Adenosine (8VA) (Chapter 5). The final part of this thesis (Chapter 6) is on understanding the mechanistic details of a DNA repair process that is due to photoinduced electron transfer in DNA photolyase, a flavoprotein. Before the electron reaches the damaged site in the DNA, the initial electron acceptor in this repair process has been speculated to be the adenine of the flavin adenine dinucleotide (FAD). We have tested this hypothesis by measuring and comparing the various kinetic parameters associated with this process by reconstituting into apo-photolyase the natural cofactor of photolyase (FAD) and an adenine modified flavin (Etheno FAD, epsilon FAD). / Chemistry

Les profils de méthylation de l’ADN sont des marques épigénétiques essentielles contrôlant l'expression génétique spécifique des tissus. Ces profils sont fidèlement reproduits par l’enzyme DNMT1 qui est dirigée par la protéine UHRF1 vers les sites CpG hémiméthylés (HM). La spécificité élevée d’UHRF1 vis-à-vis de ces sites CpG HM est liée à la capacité de son domaine SRA de basculer sélectivement les résidus méthylcytosine (mC). Par conséquent, la compréhension de la capacité d’UHRF1 à lire les séquences d'ADN et de basculer leurs résidus mC est une question importante en épigénétique moléculaire. Dans le présent travail, nous avons utilisé des analogues de nucléobases sensibles à l'environnement pour étudier le basculement de base induit par SRA. Nous avons découvert qu’un étiquetage par la 2-thiényl-3-hydroxychromone (3HCnt) à proximité de la cible CpG méthylée, permet le suivi de ce basculement SRA-induit de mC et de sa dynamique. Les spectroscopies de fluorescence à l'état stationnaire et de "stopped flow" ont montré des différences significatives entre les ADNs HM et non méthylé (NM) vis-à-vis de la reconnaissance et la cinétique de liaison du SRA. Effet, nous avons montré que SRA est capable de se lier et de glisser avec une cinétique rapide sur le duplex NM, en accord avec le rôle de lecteur d’UHRF1. Par contre, la cinétique de basculement de mC s’avère beaucoup plus lente, ce qui augmente sensiblement la durée de vie d’UHRF1 lié à un site CpG hémi-méthylé et donc la probabilité de recruter DNMT1 afin de dupliquer fidèlement le profil de méthylation de l’ADN. Nous avons ainsi obtenu pour la première fois un test capable de suivre le basculement de la base induit par UHRF1, ce qui nous a permis de proposer un mécanisme pour le recrutement de DNMT1 par UHRF1 sur les sites HM. / DNA methylation patterns are key epigenetic marks which control tissue specific gene expression. These patterns are faithfully replicated by the DNMT1 enzyme which is directed by the UHRF1 protein to hemi-methylated (HM) CpG sites. The high specificity of UHRF1 to HM CpG sites is related to the ability of its SRA domain to selectively flip methylcytosine (mC) residues. Therefore, the understanding of how UHRF1 reads DNA sequences and flips mC residues is an important question in molecular epigenetics. In the present work, we apply environment-sensitive nucleobase analogues to study the SRA-induced base flipping. We found that only labelling by 2-thienyl-3-hydroxychromone (3HCnt) outside but close to the target methylated CpG allows monitoring the SRA-induced mC-flipping and its dynamics. Fluorescence steady-state spectroscopy and stopped flow measurements showed significant differences in the recognition and binding kinetics of SRA for HM and non-methylated (NM) DNA. Indeed, SRA was found to bind and slide with fast kinetics on NM duplexes, in line with the reader role of UHRF1. In contrast, the kinetics of mC flipping was found to be much slower, substantially increasing the lifetime of UHRF1 bound to a CpG site in HM duplexes and thus, the probability of recruiting DNMT1 in order to faithfully duplicate the DNA methylation profile. Therefore, we proposed for the first time an assay able to sensitively monitor the UHRF1-induced base flipping, which helped us to provide a possible mechanism for the UHRF1 directing function on DNMT1.

Non-covalent interactions including nucleobase hydrogen bonding and phosphonium/ammonium ionic aggregation were studied in block and random polymers synthesized using controlled radical polymerization techniques such as nitroxide mediated polymerization (NMP) and reversible addition-fragmentation chain transfer polymerization (RAFT). Non-covalent interactions were expected to increase the effective molecular weight of the polymeric precursors through intermolecular associations and to induce microphase separation. The influence of non-covalent association on the structure/property relationships of these materials were studied in terms of physical properties (tensile, DMA, rheology) as well as morphological studies (AFM, SAXS). Ionic interactions, which possess stronger interaction energies than hydrogen bonds (~150 kJ/mol) were studied in the context of phosphonium-containing acrylate triblock (ABA) copolymers and random copolymers. Phosphonium-containing ionic liquid monomers with different alkyl substituent lengths and counterions enabled an investigation of the effects of ionic aggregation of phosphonium cations on the polymer physical properties. The polymerization of styrenic phosphonium-containing ionic liquid monomers using a difunctional alkoxyamine initiator, DEPN2, afforded an ABA triblock copolymer with an n-butyl acrylate soft center block and symmetric phosphonium-containing external reinforcing blocks. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) of triblock copolymers revealed pronounced microphase separation at the nanoscale. Phosphonium aggregation governed block copolymer flow activation energies. In random copolymers, the phosphonium cations only weakly aggregated, which strongly depended on the length of alkyl substituents and the type of counterions. Acrylate random copolymers consisting of quaternary ammonium functionalities were synthesized using reversible addition-fragmentation chain transfer polymerization (RAFT). The obtained copolymers possessed controlled compositions and narrow molecular weight distributions with molecular weights ranging from Mn =50,000 to 170,000 g/mol. DMA evidenced the weak aggregation of ammonium cations in the solid state. Additionally, this ionomer was salt-responsive in NaCl aqueous solutions. Hydrogen bonding, a dynamic interaction with intermediate enthalpies (10-40 kJ/mol) was introduced through complementary heterocyclic DNA nucleobases such as adenine, thymine and uracil. Our investigations in this field have focused on the use of DNA nucleobase pair interactions to control polymer self-assembly and rheological behavior. Novel acrylic adenine- and thymine-containing monomers were synthesized from aza-Michael addition reaction. The long alkyl spacers between nucleobase and polymer backbone afforded structural flexibility in self-assembly process. Adenine-containing polyacrylates exhibited unique morphologies due to adenine-adenine π-π interactions. The complementary hydrogen bonding of adenine and thymine resulted in disruption of adenine-adenine π-π interactions, leading to lower plateau modulus and lower softening temperatures. Moreover, hydrogen bonding interactions enabled the compatibilization of complementary hydrogen bonding guest molecules such as uracil phosphonium chloride. / Ph. D.