<p>DNA nanotechnology has provided programming construction of various nanostructures at nanometer-level precision over the last three decades. DNA self-assembly is usually implemented by annealing process in bulk solution. In recent several years, a new method thrives by fabricating two-dimensional (2D) nanostructures on solid surfaces. My researches mainly focus on this field, surface-assisted DNA assembly driven by base stacking. I have developed methods to fabricate DNA 2D networks via isothermal assembly on mica surfaces. I have further explored the applications to realize quasicrystal fabrication and nanoparticles (NPs) patterning.</p><p><br></p> <p>In this dissertation, I have developed a strategy to assemble DNA structures with 1 or 2 pair(s) of blunt ends. Such weak interactions cannot hold DNA motifs together in solution. However, with DNA-surface attractions, DNA motifs can assemble into large nanostructures on solid surface. Further studies reveal that the DNA-surface attractions can be controlled by the variety and concentration of cation in the bulk solution. Moreover, DNA nanostructures can be fabricated at very low motif concentrations, at which traditional solution assembly cannot render large nanostructures. Finally, assembly time course is also studied to reveal a superfast process for surface-assisted method compared with solution assembly.</p><p><br></p> <p>Based on this approach, I have extended my research scope from 1D to 2D structures assembled from various DNA motifs. In my studies, I have successfully realized conformational change regulated by DNA-surface interaction and steric effect. By introduction of DNA duplex “bridges” and unpaired nucleotide (nt) spacers, we can control the flexibility/rigidity of DNA nanomotifs, which helps to fabricate more delicate dodecagonal quasicrystals. The key point is to design the length of spacers. For 6-point-star motif, a rigid structure is required so that only 1-nt spacers are added. On the other hand, 3-nt spacers are incorporated to enable an inter-branch angle change from 60° to 90° for a more flexible 5-point-star motif. By tuning the ratio of 5 and 6 -point-star motifs in solution, we can obtain 2D networks from snub square tiling, dodecagonal tiling, a mixture of dodecagonal tiling and triangular tiling, and triangular tiling.</p><p><br></p> Finally, I have explored the applications of my assembly method for patterning NPs. Tetragonal and hexagonal DNA 2D networks have been fabricated on mica surfaces and served as templates. Then modify the surfaces with positively-charged “glues”, <i>e.g.</i> poly-L-lysine (PLL) or Ni²⁺. After that, various NPs have been patterned into designated lattices, including individual DNA nanomotifs, gold NPs (AuNPs), proteins, and silica complexes. Observed NP lattices and fast Fourier Transform (FFT) patterns have demonstrated the DNA networks’ patterning effect on NPs.

Ces travaux de thèse concernent la mise en place de nouvelles méthodologies de synthèse de porphyrines meso-substituées. Certaines porphyrines ont été synthétisées dans l’optique de réaliser des études d’assemblage sur surface, après post-fonctionnalisation ou non, dans le cadre de plusieurs collaborations internationales. D’autres porphyrines, en revanche, ont servi de modèles pour évaluer le potentiel d’application des nouvelles méthodologies proposées. Enfin, durant ces travaux, nous avons pu aussi mettre en œuvre une nouvelle méthodologie de synthèse permettant l’accès à des hexaphyrines meso substituées, avec des degrés de symétrie alors jamais décrits pour de tels composés. Le premier chapitre de ce manuscrit fait le point sur les caractéristiques, la caractérisation et la réactivité des porphyrines et des hexaphyrines. Le second chapitre propose quant à lui, après un état de l’art sur les méthodes de synthèse des macrocycles concernés, d’exposer les méthodologies de synthèse développées au cours de ces travaux pour les alkyle-porphyrines A4, puis une méthode non-scrambling appliquée à la synthèse de porphyrines de plus bas degré de symétrie, et enfin d’hexaphyrines. Le dernier chapitre fait état de l’utilisation de ces chromophores dans des procédés d’assemblage ainsi que leurs fonctionnalisations éventuelles pour l’intégration à ces procédés. / This thesis focuses on the development of new meso-substituted porphyrin synthetic methodologies. Some porphyrins were synthesized from the perspective of assembly studies on surfaces after postfunctionalization or not, in the context of several international collaborations. Other porphyrins however served as a model to evaluate the application potential of the proposed new methodologies. Finally, during this work we could also implement a new synthetic methodology allowing access to hexaphyrines meso substituted with degrees of symmetry never described for such compounds.The first chapter of this manuscript reports on the properties, characterization and reactivity of porphyrins and hexaphyrines. The second chapter provides, after a state of the art description on methods of synthesis of macrocycles concerned, exposing synthetic methodologies developed in the heart of this work for alkyl porphyrins A4 then a non-scrambling method applied to porphyrins with lower symmetry degree and finally hexaphyrines. The last chapter refers to the use of these chromophores in assembly processes and their possible functionalization for integrating these processes.

<p>Extracellular matrix (ECM) creates high-resolution chemical patterns, by assembling simple molecules with nm-scale features (e.g., carbohydrates, nucleotides, amino acids) into complex structures up to micrometers and extending to even larger scales across tissues (e.g., glycans, DNA, proteins), capable of carrying out the diverse and complex cellular functions. Mimicking the complexity of such biological systems requires precise control over the chemical patterning on substrates that exhibit physiochemical properties similar to biological systems (such as hydrogels). Although hydrogels provide tunable physiochemical properties suitable for biological applications; it is a porous material where pore sizes can range from 30 nm to greater than 1000 nm. Due to this structural heterogeneity, chemical patterning below the length scale of this heterogeneity is very challenging.</p> <p>Here, we demonstrate a new assembly system for generating a nanostructured presentation of carbohydrates on the hydrogel surface. This approach is based on the striped phases assembly of functional alkanes where 1-nm resolution functional patterns are readily assembled on substrates such as highly ordered pyrolytic graphite (HOPG). In this assembly, molecules are stabilized by noncovalent interactions, including alkyl-pi interactions underlying the HOPG, van der Waals interaction between the adjacent alkyl chains, and hydrogen bonding between polar head groups. Topochemical polymerization converts internal diynes into conjugated polydiacetylenes (PDAs). PDAs can also be utilized to covalently attach the striped pattern to polyacrylamide hydrogels through free radical chemistry.</p> <p>Here, we synthesize new amphiphiles with carbohydrate headgroups (N-acetyl-D-glucosamine (GlcNAc), and D-glucuronic acid (GlcA)), assembled into striped phases on HOPG and covalently transfer to polyacrylamide hydrogels. GlcNAc binds to wheat germ agglutinin (WGA), a lectin that binds specifically in a multivalent fashion (dissociation constant KD in nm range) to GlcNAc. We show that GlcNAc striped phases generate highly selective interactions with wheat germ agglutinin (WGA) but do not induce specific binding with concanavalin A (another lectin molecule that does not target GlcNAc). We further demonstrate that WGA binding affinity can be modulated by shifting the position of diacetylenes that bring the polymer backbone closer to the GlcNAc, increasing the effecting local concentration of carbohydrates.</p> <p>We investigated the possibility of using sPDA for secondary functionalization with complex biological molecules (such as biotin and cRGD) to mimic the ECM composition closely. The unusual reactivity of the sPDA backbones during the covalent transfer of the striped phase monolayer to hydrogels illustrates the potential of sPDA reactivity azides. In this work, we show that the addition of substituted azide molecules to sPDA-functionalized hydrogels produces a decrease in the fluorescence of the sPDA monolayer. Since these reactions are occurring on porous hydrogel surfaces characterization using techniques such as IR or NMR is difficult. We carried out further solution-phase reactions using a soluble PDA where PDA UV-vis absorption spectra red-shift after the reaction between the PDA backbone and azide. These experiments support the hypothesis of sPDA and azide click reaction.</p>