Le but de ce travail était de développer des sondes oligonucléotidiques liées à des marqueurs fluorescents émettant des signaux modifiés lors de l'hybridation avec des séquences complémentaires. Des conjugués ODNs-cyanines originaux ont été développés. L'influence de différents paramètres sur le signal fluorescent émis par la sonde ont été étudiés : position de liaisons des marqueurs à l'ODN (5'- ou internucléotidique), structure des cyanines, stéréochimie. Un nouveau réactif de phosphorylation des ODNs a été mis au point et utilisé pour la synthèse des conjugués marqués en position 5'.<br> D'autres conjugués comportant à leur extrémité 5' deux marqueurs identiques possédant des propriétés intercalantes : thiazole orange, pyrène ou pérylène ont été obtenus. Les interactions entre les deux marqueurs varient lors de l?hybridation de la sonde avec la séquence complémentaire, induisant une modification du signal fluorescent dont la nature et l'intensité dépendent du marqueur considéré

Carbocyanine dyes are organic compounds containing chains of conjugated methine groups with electron-donating and electron-withdrawing substituents at the terminal heterocycles of the general formula [R1-(CH)n-R2]+X-. The synthetic methodology and optical properties of carbocyanines will be discussed. This thesis consists of two parts: (A) synthesis and optical properties of novel carbocyanine dyes substituted with various amines and the synthesis of unsymmetrical carbocyanine dyes containing monofunctional groups for bioconjugation. (B) synthesis of heptamethine carbocyanine dyes to be used for image-guided surgery. In part A, the synthesis of carbocyanine dyes functionalized with various amines and studies of their optical properties with respect to absorbance, fluorescence, quantum yield and extinction coefficient will be presented. These property studies will aid in designing efficient dyes for future biomedical applications. Part A will also include a one pot synthesis of unsymmetrical carbocyanine dyes functionalized with mono carboxylic acid chains, useful for biomolecule (i.e. proteins, amino acids, etc.) conjugation. Part B will describe the synthesis of novel carbocyanine dyes to be used for cancer image-guided surgery. Cancers are thus far incurable diseases, i.e. there are no drugs currently available to cure cancer; however, by designing a dye to visualize tumor cells will greatly increase the efficiency of cancer removal and hopefully increase the survival rate of cancer patients. The dyes reported in this thesis are superior to commercially available dyes used to visualize and identify various tumors invisible to the naked eye of surgeons with regards to biodistribution and clearance through kidney filtration.

Heptamethine cyanine dyes are attractive compounds for imaging purposes in biomedical applications because of their chemical and photophysical properties exhibited in the near-infrared region. A series of meso amino-substituted heptamethine cyanine dyes with indolenine, benz[e]indolenine and benz[c,d]indolenine heterocyclic moieties were synthesized and their spectral properties including fluorescence quntum yield were investigated in ethanol and ethanol/water mixture. Upon substitution with amines, the absorption maxima of the dyes shifted to the lower wavelength region (~600 nm), showed larger Stokes shifts and stronger fluorescence which can be attributed to an excited state intramolecular charge transfer (ICT). High quantum yields were observed for primary amine derivatives and lower quantum yields were observed for secondary amine derivatives. Fluorescence quantum yields are greater for dyes with 3H-indolenine terminal moieties than for dyes with benz[e]indolenine end groups. Benz[c,d]indolenine based heptamethine cyanine dyes exhibited the lowest quantum yield due to aggregation in solution. In general, the benz[e]indolenine hepatemethine cyanines showed high Stokes shifts compared to indolenine dyes. For the meso-chloro dyes, the absorption maxima for the dyes shifted bathochromically in the order of indolenine, benz[e]indolenine and benz[c,d]indolenine.

In part A, the effect of varying short-chain alkyl substitution on the spectroscopic properties of cyanine dyes was examined. Molar absorptivities and quantum yields were determined for groups of pentamethine and heptamethine dyes for which the substitution of the indole nitrogen was varied. For both sets of dyes, increasing alkyl chain length did not significantly change quantum yield or molar absorptivity. These results may be useful in designing new cyanine dyes. In part B, the effect of structure on the suitability of 2,4,6-trisubstituted pyridines as color pH indicators was studied by determining spectral effects of protonation, molar absorptivities, pKa values, and the structural origin of the spectral behavior. Good color indicating properties result from aniline substitution at the 4 position of pyridine and electron donating substitution at the 2 and 6 positions of pyridine, which provide a strong red shift in the spectra and greater red shifted peak absorptivity, respectively.

Material development is necessary before all-optical signal processing (AOSP) can be realized. Traditional AOSP will require materials with a large magnitude of the real part of the third-order polarizability, while having a small imaginary magnitude of third-order polarizability. The aim of this thesis is to investigate the potential for polymethine dyes to be used for AOSP applications. The basic structure of a polymethine dye was synthetically modified in a variety of positions to observe the effects upon the linear and nonlinear optical properties. The modifications included variation in the terminal group, substituents in the polymethine bridge, and exchange of the counterion. The dyes were generally synthesized using the Vilsmeyer-Haack reaction to form simple polymethine precursors, and then complexity was added by performing the Knoevenagel condensation with various acceptors and the polymethine precursor. Ion metathesis was often employed to exchange the initial counterion for a counterion that provided increased solubility in common organic solvents. The third-order nonlinear optical polarizabilities were characterized by Dr. Joel Hales who used the open- and closed-aperture Z-scan technique at 1300 nm and non-degenerate two-photon absorption experiments to identify the position of the two-photon absorption bands.

Small molecules interacting with DNA is an emerging theme in scientific research due to its specificity and minimal side-effect. Moreover, a large amount of research has been done on finding compounds that can stabilize G-quadruplex DNA, a non-canonical secondary DNA structure, to inhibit cancerous cell proliferation. G-quadruplex DNA is found in the guanine-rich region of the chromosome that has an important role in protecting chromosomes from unwinding, participate in gene expression, contribute in the control replication of cells and more. In this research, rationally designed, synthetic cyanine dye derivatives, which were tested under physiologically relevant conditions, were found to selectively bind to G-quadruplex over duplex DNA and are favored to one structure over another. The interactions were observed using UV-Vis thermal melting, fluorescence titration, circular dichroism titration, and surface plasmon resonance analysis. For fluorescence and selectivity properties, cyanine dyes, therefore, have the potential to become the detections and/or therapeutic drugs to target cancers and many other fatal diseases.

Mechanosensitive (MS) channels are a class of ion channels which are gated by membrane stretch. The mechanosensitive channel of large conductance (MscL) of the bacterium E.coli has become a prototype MS channel for studying structure-function relationships in this class of ion channels. MscL homologues have commonly been found in Gram-negative and Gram-positive bacterial strains forming a sub-family of a larger family of MS class of ion channels encompassing prokaryotes (bacteria and archaea) as well as cell-walled eukaryotes (fungi and plants). MscL and its homologues have been found to play an important role in osmoregulation of bacterial cells. Though the MS channels of bacteria have been thoroughly studied, little is known about the pharmacology of these channels. This thesis has one general aim, that is, to identify compounds which are able to gate and/or alter the gating of the MS channels of bacteria in particular, the MscL of E. coli. Using the patch-clamp technique, potential compounds mostly identified via in-silico techniques were examined to observe the effects on MscL reconstituted in artificial lipid membranes and MscS in giant bacterial spheroplasts. The compounds were tested for the ability to spontaneously gate the MscL and MscS and/or alter the Boltzmann distribution parameters of the MscL, indicative of an effect on the gating of MscL. Compounds showing potential as MscL activators were then examined for in-vivo effects using different growth assays. The effects of parabens, gallates, eriochrome cyanine R, brilliant green, deoxycholic acid are reported. Of these compounds, parabens and eriochrome cyanine R showed the most encouraging results. Identification of MS channel gate ligands not only benefits structural studies as tetrodotoxin has for the voltage-sensitive sodium channel, these compounds could also V potentially serve as base compounds for novel antibiotics which would target the MS channels of bacteria. Since the MS channels of bacteria serve as safety valves for the bacterium, gating during exposure to a hypo-osmotic challenge such as rain to release excessive cellular turgor, a pharmacological agent that could impair the gating of the MS channels releasing essential cytoplasmic osmolytes, would cause the growth impairment or death of the bacterium. With the rise in multi-drug resistant bacteria, continual development of novel antibiotics is crucial.

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.

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.

Cyanine dyes are attractive photosensitizers for photodynamic therapy due to their ease of structure modification and intense absorption in the near-infrared range. Photosensitizers that can bind to DNA and absorb at long enough wavelengths of light to deeply penetrate biological tissue are in high demand for treatment of cancer and other diseases. The following study analyzes the DNA interactions of three pentamethine cyanine dyes with very similar structures, all of which absorb light at wavelengths longer than 800 nm. The work described involves an extensive study of the photocleavage abilities and DNA binding characteristics of these dyes. Our lead compound was a bromophenyl meso substituted symmetrical quinoline cyanine dye. Spectroscopic data, gel electrophoresis experiments and other studies were used to provide evidence of DNA binding mode, ROS production, and of dye-sensitized DNA photocleavage at the unprecedented wavelength of 850 nm.