This research serves as a meticulous examination into cross-conjugated materials and how alterations of the frontier molecular orbitals can be utilized for applications in "chemical tongue" organic sensing devices. With conjugated materials being used in the development of new sensory devices for detection of metals, bacteria, and chemical warfare agents, the field of organic sensing is growing faster than ever. The purpose of this dissertation is to provide a precedence for the synthesis of new cross-conjugated compounds and outline potential applications of these materials as chemical sensors and molecular probes.

The phosphatidylinositol polyphosphates play a fundamental role in intracellular signalling. Of particular importance is phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P₃], which acts by recruiting effector proteins to the cell membrane. PtdIns(3,4,5)P₃ interacts with its protein targets through selective binding domains that include the pleckstrin homology (PH) domain. The PH-domain-containing kinase, protein kinase B (PKB/Akt), which interacts with PtdIns(3,4,5)P₃, is upregulated in ~15 human malignancies. Significantly, inhibition of the PtdIns(3,4,5)P₃-PKB interaction has proved viable as a point of therapeutic intervention. There is currently a lack of small molecule probes that selectively interact with a given PH domain. Consequently, it is impossible to dissect the cellular function of PH-domain-containing proteins at a molecular level. To address this problem, we have designed and synthesised a number of derivatives of the PtdIns(3,4,5)P₃ inositol head-group – Ins(1,3,4,5)P₄. Replacement of the 5-position phosphate with a range of phosphate bioisosteres afforded compounds that displayed no binding affinity for the PH-domain of general receptor for phosphoinositides 1 (GRP1). However, it was shown that the 5-position sulfamate analogue displayed selectivity for the PH-domain of PKB. The methylphosphate biosiostere at the 1-position displayed binding for both the GRP1 PH-domain as well as the PKB PH-domain. These results demonstrate that subtle modification of the Ins(1,3,4,5)P₄ structure allows the synthesis of compounds that interact selectively with a given PH domain. We will now use these results for the synthesis of a second generation of compounds with improved PH-domain affinity and selectivity.

Cette thèse traite de la conception et mise en œuvre d’espaceurs auto-effondrables novateurs pour une utilisation dans des sondes d’activité enzymatique in vivo.La première partie détaille la synthèse et la validation in vitro d’espaceurs cyclisant, couplant l’activité d’un aminopeptidase à la libération d’un phénol. Les sondes fluorogènes modulaires basées sur ces espaceurs 1,2-diamine sont très robustes (demi-vie > 560 h), mais sont rapidement enzymatiquement hydrolysées, et puis relâchent rapidement (demi-temps ~ 3 min) un fluorophore ESIPT insoluble et exceptionnellement photostable.Ces sondes ont une excellente sensibilité (rapport signal:contrôle > 3000:1), et fournissent la première démonstration d’un système macroscopiquement binaire éteint–ALLUMÉ, pour la libération de phénols sous activité d’aminopeptidases. Ce système pourrait permettre de faire de l’imagerie moléculaire ultra-sensible d’une gamme d’exopeptidases. Ces espaceurs pourraient également servir dans des sondes comportant d’autres fluorophores phénoliques, dans des promédicaments de phénols/alcools activés par des peptidases spécifiques (thérapies ciblées), ou comme adaptateurs chimiques en générale.La deuxième partie détaille les synthèses de deux familles d’espaceurs tautomérisant/éliminant pour utilisation dans des sondes magnétogènes d’activité de glycosidases. Les premières architectures substrat-espaceur basées sur des 2-furanols et des carbimidates cycliques ont été explorées. Notamment, des glycosides 2-furanoliques ont été abordés comme espaceurs énergétiques alternatifs aux quinone méthydes, et des carbimidates ont été explorés comme espaceurs pour ligands modèles des sondes promagnétiques. / This thesis concerns the design and implementation of novel auto-immolative spacers for use in probes for enzymatic activity in vivo.The first part relates the development and in vitro validation of cyclisation spacers which couple the action of an aminopeptidase to the release of a phenol. The modular three-component fluorogenic probes based on these 1,2-diamine spacers are very robust (halflife > 560 h), but are also rapidly enzymatically processed, and quickly (halftime ~3 min) release an exceptionally photostable, insoluble ESIPT fluorophore. The probes have excellent detection sensitivity relative to current methods (signal to control ratio > 3000:1), and provide the first demonstration of a macroscopically binary off–ON system for phenol-releasing probes of aminopeptidase activity. The probe system may allow the exceptionally sensitive, ESIPT-based molecular imaging of a range of exopeptidases. The spacers may also be applied in off ON peptidase probes of other phenolic fluorophores, to peptidase-specific phenol/alcohol prodrugs for targeted therapy, or more generally in chemical adapter technologies.In the second part, two novel families of auto-immolative elimination/tautomerisation spacers were designed for use in three-component off ON magnetogenic probes sensing glycosidase activity. The first known substrate-spacer designs based on 2-hydroxyfurans and on carbimidates were explored. Notably, 2 furanol glycosides were synthesised in pursuit of high-energy alternatives to quinone methides, and a general method for preparing model carbimidate-bearing ligands for pro-magnetic probes was elaborated.

This work concerns the development and characterization of molecular probes that respond to a chemical analyte in a liquid sample by turning from a diamagnetic to a paramagnetic state (off-on mode).With the aim of designing these tools, we focused on iron(II) chelates of bicyclic bispidines as they promised, among others, sufficient probe stability, even in competitive media like water. This manuscript describes new robust synthetic protocols for their large-scale preparation. Synthesized bispidine-iron(II) complexes were thoroughly characterized in solution (1D/2D NMR, MS, UV-Vis, CV) and in the solid state (X-ray and SQUID). In particular, I report here the first diamagnetic, low spin examples thereof, as well as pairs of structurally related diamagnetic-paramagnetic chelates. It now enables the design of responsive probes for various (bio)-chemical targets (including enzyme biomarkers), accessible by one-step functionalization of a key synthetic intermediate with suitable trigger moieties. The first two such probes are described herein, which respond to the presence of a particular kind of anion or a change in the pH.In addition in the course of my work, the unprecedented radioactive iron(II) (Fe-59 isotope) complex of a model water-insoluble ligand was prepared and used in an initial biodistribution study in mice. This original protocol can now be directly adapted to virtually all iron(II)-based probe candidates. Furthermore, the relaxivity data obtained for model MRI-silent and MRI-active chelates, in conjunction with the in vivo behavior of the active form in mice, bode well for a creation of an MRI probe functioning in a true off-on mode.Methodologies and molecular designs described herein enable the development of solution-operating magnetogenic molecular probes, which until now have not been synthesized. The availability of such tools would open up numerous perspectives for technological, environmental and biomedical applications.

De nos jours, le domaine de la thermoplasmonique subit un développement très rapide. Ce domaine est basé sur l’amplification de la lumière absorbée par la nanoparticule métallique qui la transforme en une nanosource thermique optiquement activée. Un des défis qu’il faudra relever en thermoplasmonique est la manipulation et la valorisation de l’énergie thermique à petite échelle. De nouvelles techniques optiques permettent d’étudier les phénomènes thermiques liés aux nanoparticules plasmoniques. Ces techniques permettent de caractériser la distribution de température autour de nanoparticules métalliques avec néanmoins une résolution spatiale limitée par la diffraction. Dans cette thèse, nous présentons une nouvelle approche d’imagerie moléculaire, basée sur la nanopolymérisation amorcée thermiquement, pour caractériser le profil de chaleur au voisinage d’une nanoparticule métallique unique photo-excitée. Cette approche repose sur une formulation thermo-polymérisable caractérisée par une température seuil Ts qui est la température à partir de laquelle aura lieu la réaction de polymérisation. Nous développons ainsi des formulations présentant des Ts différentes. Après l’irradiation de la nanoparticule couverte par la solution thermo-polymérisable, la coquille de polymère créée est l’empreinte des zones où la photoconversion a induit une température supérieure à Ts. Nous démontrons la capacité de cette méthode à cartographier le champ thermique induit autour de la nanoparticule avec une résolution de l’ordre de dizaine de nanomètres (mieux que 35 nm) / Nowadays, the thermoplasmonic field undergoes a very interesting applications development thanks to the amplification of the light absorbed by the metal nanoparticle, which makes it an ideal nanosource of heat controlled by light. Because of this applications development, one of the challenges is to control and manipulate the thermal energy on a small scale.New optical techniques are dedicated to studying the thermal phenomenon induced by plasmonic nanoparticles. These techniques show different capacities to quantify and characterize the heat generated and the temperature distribution around nanoparticles. But the spatial resolution achieved is still limited by diffraction.In this thesis, we present a new molecular imaging approach, which is based on the nanopolymerization reaction thermally induced to characterize the heat profile in the vicinity of a single photoexcited nanoparticle. This approach is based on a thermo-polymerizable formulation with specific temperature threshold Tth (the temperature required to induce polymerization reaction). We develop formulations with different Tth. After irradiation of the nanoparticle covered by the thermo-polymerizable solution, the polymer shell created is the impression of areas where the photoconversion induced a temperature higher than Tth. We demonstrate the ability of this method to map the thermal field induced around the nanoparticle with a resolution better than 35 nm

Ce travail de thèse concerne la conception, la synthèse et l’étude de sondes luminescentes appliquées à la reconnaissance d’anions d’intérêt biologique. En effet, certains anions sont impliqués dans de nombreux mécanismes biologiques, et disposer d’outils pour leur détection permettra de mieux comprendre les processus mis en jeu. Nous nous sommes intéressés notamment au glutamate, principal neurotransmetteur chez les vertébrés, ainsi qu’aux dérivés de phosphates. Les sondes luminescentes que nous avons mises au point comprennent toutes un complexe de ruthénium (II) comme luminophore. Les premiers travaux décrits dans ce manuscrit concernent des sondes permettant la détection des espèces ciblées en milieu organique. Ils ont permis dans un premier temps de mieux comprendre quelles étaient les interactions mises en jeu lors de la reconnaissance des cibles, mais aussi de mieux imaginer la structure des complexes formés. Les chapitres suivant traitent de la conception, de la préparation et de l’étude de sondes optimisées grâce aux résultats de cette première partie. Nous avons ainsi pu synthétiser plusieurs sondes moléculaires capables de détecter sélectivement l’ATP, l’ADP et le glutamate dans des conditions physiologiques. / This work deals with the design, synthesis and study of molecular probes applied to the detection of anions of biological interest. Indeed, some anions are involved in several biological mechanisms and having tools for their recognition will allow a better understanding of these processes. We focused mainly on glutamate, the main vertebrate neurotransmitter, and on phosphate derivatives. All the probes we designed contain a ruthenium (II) complex as a luminescent moiety. The first part of this work examines various probes applied to the detection of our targets in organic media. This study allowed us to gain a better understanding of the interactions involved in anion complexation and of the structure of the complexes formed. Based on those results, the final chapters describe the design, synthesis and study of new, optimized probes. We have thus obtained several probes, able to detect ATP, ADP and glutamate with a good selectivity in physiological conditions.

Cette thèse décrit le développement et de la caractérisation de sondes moléculaires répondant à des analytes chimiques en solution par le passage d’un état diamagnétique à un état paramagnétique (mode off-on).Dans le but de concevoir de tels outils, nous avons focalisé notre attention sur les chélates de fer(II) avec des ligands de type bispidine bicyclique puisqu’ils présentent, entre autres, une stabilité suffisante même en milieux compétitifs comme l’eau. Ce manuscrit décrit des protocoles synthétiques robustes pour leurs préparations à grande échelle. Les complexes synthétisés ont été entièrement caractérisé en solution (RMN 1D/2D, MS, UV-Vis, CV) et dans l’état solide (rayon X et SQUID). Je suis notamment parvenu à synthétiser le premier exemple de complexe bispidine-fer(II) diamagnétique, bas spin, ainsi qu’à proposer des paires de chélates diamagnétique-paramagnétique aux structures connexes. Nous avons donc à notre disposition un système magnétique off-on valide, qui permet le design de sondes répondant à un stimulus (bio)-chimiques (biomarqueurs enzymatiques par ex.) par fonctionnalisation d’un synthon clé en une seule étape. Les deux premières sondes de ce type sont décrites ici, une répondant à la présence d’anions particuliers et l’autre répondant au pH.Au cours de ce travail, nous avons également mis au point la préparation du tout premier complexe de fer(II) radioactif avec un ligand insoluble en milieu aqueux et nous l’avons utilisé pour faire une étude préliminaire de biodistribution chez la souris. Ce protocole original pourrait être adapté pour virtuellement toute sonde à base de complexes de fer(II). Les données de relaxivité obtenues pour les modes silencieux et actif en IRM en conjonction avec le comportement in vivo de la forme active chez la souris semblent être prometteuses quant à la création d’une sonde IRM fonctionnant sur le principe du mode off-on.Les méthodologies et designs moléculaires présentés ici ouvrent le champ au développement de sondes moléculaires magnétogéniques opérationnelles en solution, qui n’avait, pour l’heure, jamais été synthétisé. L’avènement de tels outils présente de nombreuses perspectives pour des applications dans les domaines technologiques, environnementales et biomédicales. / This work concerns the development and characterization of molecular probes that respond to a chemical analyte in a liquid sample by turning from a diamagnetic to a paramagnetic state (off-on mode).With the aim of designing these tools, we focused on iron(II) chelates of bicyclic bispidines as they promised, among others, sufficient probe stability, even in competitive media like water. This manuscript describes new robust synthetic protocols for their large-scale preparation. Synthesized bispidine-iron(II) complexes were thoroughly characterized in solution (1D/2D NMR, MS, UV-Vis, CV) and in the solid state (X-ray and SQUID). In particular, I report here the first diamagnetic, low spin examples thereof, as well as pairs of structurally related diamagnetic-paramagnetic chelates. It now enables the design of responsive probes for various (bio)-chemical targets (including enzyme biomarkers), accessible by one-step functionalization of a key synthetic intermediate with suitable trigger moieties. The first two such probes are described herein, which respond to the presence of a particular kind of anion or a change in the pH.In addition in the course of my work, the unprecedented radioactive iron(II) (Fe-59 isotope) complex of a model water-insoluble ligand was prepared and used in an initial biodistribution study in mice. This original protocol can now be directly adapted to virtually all iron(II)-based probe candidates. Furthermore, the relaxivity data obtained for model MRI-silent and MRI-active chelates, in conjunction with the in vivo behavior of the active form in mice, bode well for a creation of an MRI probe functioning in a true off-on mode.Methodologies and molecular designs described herein enable the development of solution-operating magnetogenic molecular probes, which until now have not been synthesized. The availability of such tools would open up numerous perspectives for technological, environmental and biomedical applications.

Detection, imaging and quantification of gene expression in living cells can provide essential information on basic biological issues and disease processes. To establish this technology, we need to develop molecular probes and cellular delivery methods to detect specific RNAs in live cells with potential for in vivo applications. In this thesis work, the major focus is placed on the development of molecular beacons and biochemical approaches (peptides etc.) to deliver such probes to different cellular compartments. These approaches are then employed to study the expression and localization of mRNAs, co-localization of mRNAs with cytoplasmic organelles and cytoskeleton, and co-localization of RNA molecules in the nuclei of living cells. Further along this direction, we were interested in developing a better understanding of the functional states of mRNAs and the fluorescent signal observed in optical imaging experiments. To acheive this goal, we altered the translational process and studied its effect on the detection of mRNAs in living cells. The results of these studies indicate that the translational state of mRNAs favors the hybridization of molecular beacon with its target sequence. This study has also provided the evidence that molecular beacons are reversibly bound to target mRNAs and the repression of the translational process can prevent molecular beacon from binding to its target mRNA. Further, using these approaches in combination with FRAP based biophysical analysis, the dynamics of endogenous RNA in living cells are studied. These studies revealed the possible subcellular organization of RNA molecules and their dynamics in living cells. The results also demonstrated the role of cytoskeleton and ATP in the mobility of specific mRNAs in the cytoplasm. In addition to optical probes, studies have been carried out to develop an MRI contrast agent using iron-oxide nanoparticles for deep tissue molecular imaging. Specifically, we have functionalized magnetic nanoparticles that are water-soluble, mono-dispersed, biocompatible, and easily adaptable for multifunctional bioconjugation of probes and ligands. We have successfully delivered magnetic nanoparticle bioconjugates into live cells and demonstrated their effect on relaxivity. We have further studied the role of coating thickness for optimization of contrast and further enhance the fundamental understanding of contrast mechanisms.

This dissertation presents a new class of cancer diagnostic agents composed of quantum dots, magnetic nanoparticles, and amphiphilic polymers. The central hypothesis is that biocompatible, amphiphilic block copolymers can be used to create multinanoparticle micellar probes with imaging capabilities and surface properties optimized for applications in cancer diagnostics. To test this hypothesis, we investigated a number of different block copolymer structures and synthetic procedures. We found that use of a poly(methyl methacrylate)-poly(ethylene oxide) polymer in conjunction with a dialysis-based procedure produced uniform probes with excellent imaging properties. We also found that the probes formed using these materials and methods were surprisingly stable, even after incubation in whole human blood for 24 hrs at 37oC. As a corollary, we hypothesized that modified polymer structures could be used to introduce functional groups for use in linking the micellar probes to biological molecules. To test this hypothesis, we used a modified version of our synthetic procedure and utilized a novel method for studying nanoparticle binding to biological molecules in real time. We found that active amine groups could be added to the polymer shell using these methods, and that surface plasmon resonance could be used for studying nanoparticle binding. In sum, this dissertation makes several contributions to the field of cancer nanotechnology. First, we provide a new encapsulation procedure and nanostructure that has promising physical and biological properties. Secondly, we provide general strategies that can be used for future nanoprobe development. Finally, we demonstrate the capability of a new method for quantitative study of probe binding characteristics. Together, these contributions drive the field of cancer nanotechnology forward by providing a deeper understanding of the relationship between surface design and behavior in biological systems.

The antibody class switch is achieved by DNA recombination between the sequences called switch (S) regions located 5' to immunoglobulin (Ig) heavy chain constant (CH) region genes. This process can be induced in cultured B cells by polyclonal stimulation and switching can be directed to specific antibody classes by certain lymphokines. These stimuli may regulate the accessibility of CH genes and their S regions to a recombinase as indicated by hypomethylation and transcriptional activity. For example, RNAs transcribed from specific unrearranged (germ-line) CH genes are induced prior to switching under conditions that promote subsequent switching to these same CH genes. The function of transcription of these germ-line CH genes is unknown. How stimuli regulate the accessibility of CHgenes is also unclear. I report in this dissertation the structure of the RNA transcribed from the unrearranged Cγ1 gene in mouse spleen cells treated with LPS plus a HeLa cell supernatant containing recombinant interleukin 4 (rIL-4). I will also show that an 150-bp region upstream of the first initiation site of germ-line γ1 RNA contains promoter and enhancer elements responsible for basal level expression and inducibility by phorbol 12-myristate 13-acetate (PMA) and synergy with IL-4 in an IgM+ B cell line, L10A6.2, and an IgG2a+B cell line, A20.3. The germ-line γ1 RNA is initiated at multiple start sites 5' to the tandem repeats of the γ1 switch (Sγ1) region. As is true for analogous RNAs transcribed from other unrearranged genes, the germ-line γ1 RNA has an I exon transcribed from the region 5' to the Sγ1 region.. The Iγ1 exon is spliced at a unique site to the Cγ1 gene. The germ-line γ1 RNA has an open-reading frame (ORF) that potentially encodes a small protein 48 amino acids in length. Elements located within the 150 bp region 5' to the first initiation site of germ-line γ1 RNA are necessary and sufficient to confer inducibility by PMA and synergy with IL-4 to a minimal thymidine kinase (TK) promoter in L10A6.2 cells but are not sufficient to confer this inducibility in A20.3 cells. Linker-scanning mutations demonstrated that these multiple elements function in a mutually dependent manner as indicated by the fact that mutation of any single element will decrease constitutive expression and inducibility by PMA and PMA plus IL-4. This 150-bp region contains several consensus sequences that bind to known or putative transcription factors, including a C/EBP binding site/IL-4 response element (in the promoter for Ia Aαkgene), four CACCC boxes, a PU box, a TGFβ inhibitory element (TIE), an interferon-αβ response element (αβIRE), and an AP-3 site. My results begin to provide a description of the mechanism of regulation of the accessibility of unrearranged germ-line Sγ1-Cγ1 gene. By activating the germ-line γ1 promoter, IL-4 induces transcription of germ-line γ1 RNA, thereby inducing accessibility of the Sγ1-Cγ1 gene. By inhibiting expression of the germ-line γ1 promoter, IFNγ and TGFβ down-regulate transcription of germ-line γ1 RNA, thus reducing the accessibility of the Sγ1-Cγ1 gene. My results also suggest that signaling via the antigen receptor on B cells may be involved in induction of switch to IgG1. Furthermore, this is the first case reported in which multiple functionally interdependent elements are needed to respond to PMA.