Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biological systems. Here we apply linear absorption, circular dichroism, and two-dimensional fluorescence spectroscopy to study the local structure and excited state dynamics of excitonically coupled cyanine dimers that are rigidly positioned within the sugar-phosphate backbones of the DNA. Dimer probes were positioned within the double-stranded DNA duplex and at the single-strand/double-stranded DNA junction to examine the positional dependence of the structural variation and fluctuations. We interpret spectroscopic measurements in terms of the Holstein vibronic dimer model, from which we obtain information about the local conformation of the dimer probe locally within their respective DNA environments. We show that the exciton-coupling strength of the dimer-DNA construct can be systematically varied with temperature below the double-stranded – single-strand DNA denaturation transition. Using time-resolve 2DFS measurements we observed long lived vibronic coherences in the system. The properties of the cyanine DNA construct we determine suggest that it may be employed as a useful model system to test fundamental concepts of protein DNA interactions and the role of electronic-vibrational coherence in electronic energy migration within exciton-coupled biomolecular arrays. This dissertation contains previously published and unpublished co-authored material.

abstract: Fluorescence spectroscopy is a powerful tool for biophysical studies due to its high sensitivity and broad availability. It is possible to detect fluorescence from single molecules allowing researchers to see the behavior of subpopulations whose presence is obscured by “bulk” collection methods. The fluorescent probes used in these experiments are affected by the solution and macromolecular environments they are in. A misunderstanding of a probe’s photophysics can lead researchers to assign observed behavior to biomolecules, when in fact the probe is responsible. On the other hand, a probe’s photophysical behavior is a signature of the environment surrounding it; it can be exploited to learn about the biomolecule(s) under study. A thorough examination of a probe’s photophysics is critical to data interpretation in both cases and is the focus of this work. This dissertation investigates the photophysical behavior of symmetric and asymmetric cyanines in a variety of solution and biomolecular environments. Using fluorescent techniques—such as time-correlated single photon counting (TCSPC) and fluorescence correlation spectroscopy (FCS)—it was found that cyanines are influenced by the local environment. In the first project, the symmetric cyanines are found to be susceptible to paramagnetic species, such as manganese(II), that enhance the intersystem crossing (ISC) rate increasing triplet blinking and accelerating photobleaching. Another project found the increase in fluorescence of Cy3 in the protein induced fluorescence enhancement (PIFE) technique is due to reduced photoisomerization caused by the proximity of protein to Cy3. The third project focused on asymmetric cyanines; their photophysical behavior has not been previously characterized. Dy630 as a free dye behaves like Cy3; it has a short lifetime and can deactivate via photoisomerization. Preliminary experiments on Dy dyes conjugated to DNA show these dyes do not photoisomerize, and do not show PIFE potential. Further research will explore other conjugation strategies, with the goal of optimizing conditions in which Dy630 can be used as the red-absorbing analogue of Cy3 for PIFE applications. In summary, this dissertation focused on photophysical investigations, the understanding of which forms the backbone of rigorous fluorescent studies and is vital to the development of the fluorescence field. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

Small-molecule inhibitors of tau fibrillization are under investigation as tools for interrogating the tau aggregation pathway and as potential therapeutic agents for Alzheimer's disease. Established inhibitors include thiacarbocyanine dyes, which can inhibit recombinant tau fibrillization in the presence of anionic surfactant aggregation inducers. In an effort to increase inhibitory potency, a cyclic bis-thiacarbocyanine molecule containing two thiacarbocyanine moieties was synthesized and characterized with respect to tau fibrillization inhibitory activity by electron microscopy and ligand aggregation state by absorbance spectroscopy. Results showed that the inhibitory activity of the bis-thiacarbocyanine was qualitatively similar to a monomeric cyanine dye, but was more potent with 50% inhibition achieved at ∼80 nM concentration. At all concentrations tested in aqueous solution, the bis-thiacarbocyanine collapsed to form a closed clamshell structure. However, the presence of tau protein selectively stabilized the open conformation. These results suggest that the inhibitory activity of bis-thiacarbocyanine results from multivalency, and reveal a route to more potent tau aggregation inhibitors.

L’objectif de cette thèse est de développer un nouveau matériau photopolymère pouvant être microstructuré dans la gamme de longueur d'onde du proche infrarouge (NIR). Le but final de ce travail est de proposer des solutions innovantes pour l'intégration de micro-optique sur les VCSELs (Vertical-Cavity Surface-Emitting Laser), sources lumineuses miniaturisées utilisées dans de nombreuses applications en optique, photonique, capteurs ou biologie. Le verrou technologique principal a consisté à développer et étudier le photopolymère adéquat pour la microfabrication déclenchée par le VCSEL. La difficulté principale tient à la longueur d'onde de photopolymérisation qui est fixé par le VCSEL et qui a obligé à développer un système moléculaire nouveau pour une polymérisation radicalaire à 780 et 850 nm. Une part importante du travail a consisté à étudier les mécanismes photophysiques et photochimiques des matériaux permettant de proposer des systèmes efficaces, sur le plan de la photophysique, de la photochimie de photopolymérisation et également une approche originale a été développée pour appréhender de façon quantitative les phénomènes de diffusion du colorant dans la matrice polymère. Sur la base des systèmes moléculaires proposés, la démonstration de l'intégration de microlentilles sur VCSEL par ce procédé innovant a pu être démontré. Les VCSELs lentillés ont été caractérisés et des propriétés très intéressantes pour la focalisation ont été démontrées. / The objective of this thesis is to develop a new photopolymer material that can be microstructured in the wavelength range of near-infrared (NIR). The ultimate aim of this work is to propose innovative solutions for micro-optical integration on VCSELs (Vertical-Cavity Surface-Emitting Laser). These miniaturized light sources are used in many applications in optics, photonics, sensors or biology. The main technological challenge was to develop and explore a new photopolymer compatible with a microfabrication initiated by the VCSEL. The main difficulty was to develop a new molecular system for radical polymerization at 780 and 850 nm, which is the wavelength emitted by the VCSEL. An important part of the work consisted to study the photophysical and photochemical mechanisms of this photopolymer in order to provide efficient systems in terms of photophysics, photochemistry of the photopolymerization. An original approach was developed to quantitatively apprehend the phenomena dye diffusion in the polymer matrix. Based on the proposed molecular systems, demonstrating the integration of microlenses on VCSELs by this innovative process could be shown. The lensed VCSELs have been characterized and very interesting properties for focusing have been demonstrated.

The molecular identity of the green emission of polyfluorene is investigated in the view point of the molecular interactions between modeled segments. The semi-empirical quantum methods, ZINDO/S and AM1 (AM1-CIS), are used in combination to provide reasonable explanations for experimental spectroscopic properties of monodisperse fluorene oligomers and fluorene oligomers with a central keto defect in dilute solutions. Applying the same method, the molecular interactions between model segments are found to exist and are significant. However, the spectroscopic property change from the molecular interactions is negligible. In addition, the effects of mechanical stress and multi-defects on fluorene oligomers are investigated. On the other hand, the redox mechanisms proposed for the oxidation of an amphiphilic cyanine (C8S3) J-aggregates immobilized at ITO electrode and the subsequent dehydrogenated dimmer formation during cyclic voltammetry based on analysis of absorption spectra during the process are verified with the combined semi-empirical quantum methods similar to the previous methods. The absorption spectra assigned by experiment for electrochemical species involved in the proposed mechanism show reasonable match to the theoretically estimated absorption energies of the corresponding simplified model systems. In addition, the standard reduction potentials of the fairly large molecules, C8S3 monomer and its dehydrogenated dimer, are pursued with quantum mechanical calculations. The free energy difference between the oxidized and reduced states of the target systems is decomposed to electronic energy, solvation energy and temperature-dependent free energies terms. Based on AM1 ground state geometries and with the corresponding temperature dependent free energies, the electronic energies and the solvation energies are each evaluated by two different methods. The electronic energies are calculated with AM1 method and DFT calculation and, also, the solvation energies are obtained based on the atomic partial charges from AM1 and DFT wavefunctions with continuum dielectric solvent approximation. The four calculation schemes from the combinations of the electronic and solvation energy estimation methods are tested with the redox compounds with various molecular weights and the estimations are compared with the corresponding experimental redox potentials. The relative redox potentials between two different redox systems are found to be reasonably estimated with the four calculation schemes. / text

No description available.

Cyanine dyes that absorb light in the near infrared to far red region of the electromagnetic spectrum are desirable as photosensitizers for photodynamic cancer therapy. Light of wavelengths in this range is able to deeply penetrate tissue allowing for practical in vivo use of these dyes. A series of three structurally similar pentamethine cyanine dyes that absorb light ~800 nm to ~500 nm was tested to determine the effects of structural influences on the yields of supercoiled DNA photo-converted to nicked or linear forms. Possible mechanisms and optimal parameters for near- quantitative DNA photocleavage with a symmetrical quinoline pentamethine cyanine dye are discussed.

A terapia fotodinâmica (PDT) consiste em introduzir no organismo um composto fotoativo (fotossensibilizador) e irradiar o local a ser tratado com a luz visível. Este procedimento permite obter a(s) forma(s) ativa(s) do composto que tem a capacidade de matar células neoplásicas, bem como fungos e bactérias. Algumas desvantagens dos fotossensibilizadores atualmente aplicados na clínica estimulam a busca de novos compostos mais adequados. Os corantes ciânicos com dois cromóforos (BCD) possuem características espectrais promissoras para aplicação em PDT. Isso estimulou a realização deste trabalho que teve como finalidade estudar as características espectrais, energéticas e de fotodecomposição dos BCD: (i) em diferentes solventes (escolhidos pela constante dielétrica $\\xi$ e capacidade de formar ligação hidrogênio), (ii) na interação com micelas, e (iii) na interação com DNA. Foram estudados $4$ isômeros de corantes ciânicos com dois cromóforos (BCD) com estrutras iguais. Estes isômeros diferem pela estrutura da parte central da molécula. Foram utilizados métodos espectroscópicos estáticos e com resolução temporal tais como absorção ótica, flash-fotólise, fluorescência, anisotropia, dicroísmo circular e calorimetria fotoacústica. Os resultados experimentais foram analisados em comparação com resultados obtidos do cálculo computacional em que foi feita a otimização geométrica das moléculas, análise de orbitais eletrônicos, dos níveis de energia e das probabilidades de transição entre estes. A partir destes dados foram construídos os espectros de absorção S-S dos corantes. Os cálculos confirmaram que a probabilidade de transição entre os níveis de energia dos BCD depende do ângulo entre os cromóforos que é determinado pela estrutura da parte central da molécula. Para um ângulo de $180^{0}$ somente uma banda de absorção está presente no espectro e para o de $90^{0}$ aparecem duas bandas de intensidades iguais. Foi mostrado que no intervalo de temperaturas $<100^{0}$ as conformações dos cromóforos de BCD no estado fundamental são trans-trans, exceto para o BCD com ângulo de $120^{0}$ entre os cromóforos em que no intervalo $0^{0}$ a $100^{0}$ ocorre a mistura das conformações trans-trans e cis-trans. Os resultados experimentais mostraram que em solventes orgânicos os BCD não formam agregados. Como suas características espectroscópicas não seguem a equação de Lippert concluímos que sua solvatação está determinada tanto pelo mecanismo não específico como específico devido as ligações hidrogênio. Os tempos de vida ($\\tau_{S1},\\tau{}_{T1}$) e rendimentos quânticos ($\\phi_{S1},\\phi{}_{T1}$) dos estados excitados singleto e tripleto dos BCD diminuíram com o aumento da constante dielétrica $\\xi$ do solvente. Entretanto o aumento da viscosidade do solvente aumentou estes parâmetros. A presença de água nos solventes orgânicos promove a formação dos agregados de BCD. Os valores de $\\tau_{S1},\\tau\\,{}_{T1}$ e $\\phi_{S1},\\phi\\,{}_{T1}$ diminuíram, provavelmente, devido a dois efeitos: diminuição da microviscosidade ao redor da molécula de BCD e agregação do BCD estimulada pela presença da água. A interação dos BCD com micelas depende da carga dos tensoativos. Para uma carga negativa houve a presença de $3$ espécies do corante dependendo da concentração das micelas: os monômeros livres, os monômeros ligados à micela e os agregados ligados a micela. O tensoativo zwiteriônico gerou duas espécies: os monômeros livres e os monômeros ligados à micela. As constantes de ligação dos BCD com micelas de LPC são da ordem $10^{7}M^{-1}$. Não houve interação com os tensoativos positivos. A interação com DNA estimula a agregação de BCD. Na presença de DNA em solução existem três espécies de BCD: os monômeros livres e ligados com DNA e os agregados de BCD na superfície do DNA. O conteúdo relativo dessas espécies depende da razão {[}BCD]/{[}DNA]. As constantes de ligação dos monômeros de todos BCD com DNA foram da ordem de E7M^{-1}$. Os valores de tau_{S1},\\tau{}_{T1}$ e $\\phi_{S1},\\phi{}_{T1}$ aumentaram com a ligação dos BCD ao DNA, o que significa que a contribuição dos processos não radiativos diminuiu em comparação a água e aos solventes orgânicos. Os BCD sofrem fotodecomposição e esta depende da presença de oxigênio. Na fotodecomposição do BCD ocorre destruição do sistema de conjugação-pi num dos cromóforos pela ligação do oxigênio singlete, formado devido a transferência de energia do estado tripleto do próprio BCD para oxigênio molecular. Os resultados obtidos (alta afinidade com sistemas biológicos e modelos, altos rendimentos quânticos do estado tripleto na interação com estes sistemas, formação de oxigênio singleto) mostram que os BCD apresentam características vantajosas para suas aplicações como fotossensibilizadores em PDT, motivo pelo qual o estudo da sua fototoxicidade e testes in vivo deve prosseguir. / Photodynamic therapy (PDT) consists in the administration of photoactive compounds (photosensitizers) in an organism with subsequent application of visible light to the area to be treated. This procedure leads to the activation of the compound which kills neoplasic cells, as well as fungus and bacteria. The photosensitizers used nowadays show some disadvantages, thus motivating the search for more effective compounds. Bichromophoric cyanine dyes (BCD) exhibit good spectral characteristics to be used in PDT, encouraging the development of this study. This work aimed at studying spectral, energetic and photodecomposition characteristics of BCD: (i) in different solvents (choosen accordingly to their dieletric constant $\\xi$ and the capacity to form hydrogen bonds), (ii) at their interaction with micelles and (iii) at their interactions with DNA. Four BCD isomers with equal chromophores and different structure of the central part of the molecule were studied. Static and time resolved spectroscopic methods such as optical absorption, fluorescence, anisotropy, circular dicroism and photoacustic calorimetry were used. Experimental results were compared with computational ones, based on geometry optimization and analysis of electronic orbital densities, energy levels and transition probabilities. This data allowed to create the BCD singlet absorption spectrum. The computer modelling confirmed that the transition probabilities depended on the angle between chromophores determined by the central structure. The $180^{0}$ BCD showed a single absorption band, while the $90^{0}$ BCD showed two bands of equal intensities. It was demonstrated that at $<100^{0}C$ BCD chromophores are present in the trans-trans form, except for the BCD with $120^{0}$ where the mixture of trans-trans and cis-trans forms was present in the $0^{0}-100^{0}C$ temperature interval. Experimental results have shown that BCD did not form aggregates in organic solvents. The BCD spectral characteristics did not followed the Lippert equation, which means that both non-specific and specific mechanisms, such as the hydrogen bond formation determined the BCD solvatation The life times ($\\tau_{S1},\\tau\\,{}_{T1}$) and quantum yields ($\\phi_{S1},\\phi\\,{}_{T1}$) of singlet and triplet excited states decreased with increase of the solvent dielectric constant $\\xi$. Though, the solvent viscosity increment caused the increase of these parameters. The addition of water to organic solvents led to BCD aggregation. The $\\tau_{S1},\\tau\\,{}_{T1}$ and $\\phi_{S1},\\phi\\,{}_{T1}$ values decreased, probably due to two effects: the decrease of microviscosity around the molecules and aggregation of BCD due to interaction with water. The interaction of BCD with micelles depended on the micelle electric charge. In the presence of negatively charged ones three species were produced in the solution: BCD free monomers, BCD aggregates bound to micelles and BCD monomers bound to micelles. Zwiterionic micelles produced two species: BCD free monomers and monomers bound to micelles. The binding constants with zwiterionic LPC micelles were $\\sim10^{6}M^{-1}$. Positively charged micelles did not interact with BCD. Interaction with DNA stimulated the BCD aggregation. Three species were produced in the solution: BCD free monomers and monomers bound to DNA and BCD aggregates bound to DNA. The relative content of these species depended on the {[}BCD]/{[}DNA] ratio. The BCD monomer to DNA binding constants were $\\sim10^{7}M^{-1}$. The $\\tau_{S1},\\tau{}_{T1}$ and $\\phi_{S1},\\phi{}_{T1}$ values increased with BCD binding to DNA, indicating that non radioactive processes decreased in comparison with pure water and homogeneous organic solvents. The BCD photodecomposition depended on the oxygen presence. This fotodecomposition occured when singlet oxygen (generated due to the energy transfer from the BCD molecule in its triplet state to molecular oxygen) interacted with one of the BCD chromophores destroying its $\\pi$-conjugation system. The obtained results (high affinity to biological and model systems, high triplet state quantum yields at interaction with these systems, singlet oxygen formation) showed that BCD possess promising characteristics for application as photosensitizers in PDT, encouraging future studies on their phototoxicity and \\textit{in vivo} tests.

Interkalatorfarbstoffe wie Thiazolorange (TO) wurden an Stelle einer internen Nucleobase in PNA eingebaut. Solche Konjugate werden als FIT-Sonden (Forced Intercalation of Thiazole Orange) bezeichnet. Bei Hybridisierung interkaliert Thiazolorange in unmittelbarer Nachbarschaft zu einem mismatch Basenpaar in einen PNA·DNA-Duplex . Diese Arbeit befasste sich zunächst mit der Entwicklung einer linearen Strategie für die Festphasensynthese von PNA. Um den Einfluss der stacking- und pairing-Partner von Thiazolorange auf Stabilität und optische Eigenschaften der entsprechenden PNA•DNA-Duplexe zu untersuchen, wurden sowohl N-terminal (x) als auch C-terminal (y) benachbarte. Basen von TO in Aeg-TO- und D-Orn-TO-Oligomeren variiert. Die durchgeführten Studien belegen, dass das Thiazolorange-Basensurrogat seine Fluoreszenzintensität bei Hybridisierung am stärksten ändert, wenn es von zwei Adenin-Bausteinen flankiert wird. In Light-up-Sonden ist TO über einen flexiblen Linker mit dem N-oder C-Terminus des Oligomers verbunden, in FIT-Sonden ist eine Base durch TO ersetzt. Beide Varianten wurde in Hybridisierungsexperimenten miteinander verglichen. / Intercalator dyes such as thiazole orange have been linked into PNA by replacing an internal nucleobase. In these conjugates the DNA stain thiazole orange (TO) was forced to intercalate next to mismatched base pairs in a PNA•DNA duplex. These conjugates were named as FIT (Forced Intercalation of Thiazole orange) probes and are used to find single base mutation. This work was first concerned with the development of a linear strategy for the solid-phase synthesis of FIT-PNA. To explore the influence of thiazole orange stacking and pairing partners on stability and optical properties of duplexes the N’-terminal (x) and C’-terminal (y) bases of thiazole orange environment were varied for both Aeg-TO and D-Orn-TO containing oligomers. The above studies showed that the fluorescence of the thiazole orange base surrogate is most responsive to hybridisation when TO is flanked by adenine-adenine. The influence of the different attachment modes was explored by the hybridization experiments.

O câncer é uma patologia responsável por um grande número de óbitos. Os tratamentos convencionais, quimioterapia e radioterapia, nem sempre são eficientes e, além disso, os efeitos colaterais são intrínsecos às terapias. A partir da década de 70 surgiu uma nova forma de terapia chamada de “terapia fotodinâmica" (“Photodynamic Therapy", PDT) que apresenta poucos efeitos colaterais quando comparada com as terapias convencionais. O princípio da PDT é introduzir no organismo um composto fotoativo e irradiar com luz visível o local a ser tratado, obtendo assim a forma ativa do composto que induz a morte das células cancerígenas. Os compostos atualmente usados em PDT possuem algumas desvantagens na sua aplicação que estimula a busca de outros compostos mais satisfatórios. Neste projeto foram estudados corantes ciânicos com dois cromóforos (BCD) que possuem boas vantagem para uso em PDT. O trabalho foi focado no estudo das características espectrais e energéticas dos BCD na interação com DNA, e o efeito da força iônica nessa interação para sugerir seu uso em fotoquimioterapia, principalmente em PDT. Foram estudados quatro BCD que se diferenciam pelo ângulo entre os cromóforos. As análises experimentais foram feitas através de métodos espectroscópicos de absorção ótica, fluorescência e dicroísmo circular, e as teóricas através de programas computacionais comerciais e um programa desenvolvido neste trabalho. Os resultados obtidos mostram que os BCD possuem alta afinidade com as moléculas de DNA, formando diferentes espécies que afetam nas características dos seus estados excitados. A presença de outros íons influencia as características dos corantes e a sua interação com DNA. Pelos resultados obtidos podemos considerar que os BCD apresentam boas características para aplicação em PDT e que estes resultados dão suporte para estudos futuros da interação destes corantes com sistemas naturais (células) e para fazer testes clínicos em animais. / Cancer is a pathology responsible for a great number of deaths. The conventional methods of treatment, chemotherapy and radiotherapy, are not always efficient, and multiple side effects are intrinsic for these therapies. In early 70’s appeared a new method called “Photodynamic Therapy" (PDT), that shows few side effects as compared with conventional therapies. The main idea of PDT is to introduce a fotoactive compound into the organism and then irradiate with visible light the site to be treated, producing the active form of the compound that induces the death of cancers cells. The compounds used for this purpose have some disadvantages in their application, which stimulates the search for best compounds. In this work were studied several cyanine dyes with two interacting chromophores (BCD), which seem advantageous for use in PDT. The aim is to study spectral and energetic features of BCD in the presence of DNA, and at various ionic strengths, to suggest their use in cancer photochemotherapy. Four BCD studied in this work were characterized by different angles between chromophores. The experimental analysis was made using various spectroscopic methods such as optical absorption, fluorescence and circular dichroism, and the theoretical treatment was based on computational programs both conventional and created in this work. The results show that BCD has high affinity with DNA molecules, forming various species thus changing the BCD excited state features. The presence of ions modifies the characteristics of dyes and their interaction with DNA. Analyzing the results we can conclude that the characteristics of BCD are promising for their application in PDT, and this makes reasonable future studies of the interaction of these dyes with natural systems such as cells culture and tumors in laboratory animals.