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Ce travail de thèse est consacré à la synthèse et la caractérisation structurale par spectroscopies RMN, IR, CD et RX de nouveaux oligomères non naturels qui s'inscrivent dans la famille des foldamères. Ils sont construits en particulier à partir d'un β-aminoacide bicyclique chiral original: l'acide (S)- ou (R)-aminobicyclo[2.2.2]octane-2-carboxylique ((S)- et (R) ABOC) que nous avons développé. Ce motif est issu d'une synthèse stéréocontrollée, dont l'étape clef est une réaction de Diels-Alder asymétrique. Après avoir montré que ce motif est un mime de coude peptidique il a été utilisé pour la synthèse de plusieurs séries d'oligomères. Deux grandes familles ont été développées: des oligourées et des oligoamides. A l'intérieur de ces familles, des homo- et des hétéro-oligomères ont été synthétisés et leur préférence conformationnelle a été définie. Les analyses RMN et les études cristallographiques ont permis de montrer qu'en fonction de leur séquence ils sont capables d'adopter plusieurs types d'hélices. Les homo-oligourées d'ABOC et des hétéro-oligourées alternant l'ABOC et des β3-aminoacides ont conduit à des hélices-12/14. Les oligoamides construits par des alternances d'ABOC et de β3-aminoacides dans un rapport 1/1 et des alternances d'ABOC et d'α-aminoacides dans un rapport 1/1 ou 1/2 ont conduit respectivement à des hélices 10/12, 16/18 et 12/14. / This thesis is devoted to the synthesis and FT-IR, CD, NMR and X-ray structural characterization of new unnatural oligomers belonging to the family of foldamers. In particular they are constructed from an original chiral bicyclic β-amino acid: (S)- and (R)-aminobicyclo[2.2.2]octane-2-carboxylic acid ((S) - and (R) ABOC ) that we have developed. This motive was obtained via a stereocontrolled synthesis using an asymmetric Diels-Alder reaction as key step. Firstly, this motive was shown to induce turn in peptide sequence and then it was used for the synthesis of several series of oligomers. Two main families were developed: oligoureas and oligoamides. Within these families, homo-and hetero-oligomers were synthesized and their conformational preferences were defined. NMR analysis and crystallographic studies have shown that depending on their sequence they are able to adopt several types of helices. ABOC homo-oligoureas and hetero-oligoureas containing both ABOC residue and β3-amino acid favor a 12/14-helix. Oligoamides with 1/1 alternation of ABOC and β3-amino acids, and heterogeneous backbones with 1/1 and 1/2 ABOC/α-amino acid residue patterns adopt 10/12-, 16/18- and 12/14-helix, respectively.

Magistro baigiamajame darbe tiriamos nevienalyčių plačiajuosčių periodinių sistemų užtvarinės savybės. Aptariamos periodinės sistemos ir jų charakteristikų skaičiavimo metodai. Nevienalyčių periodinių savybių tyrimui panaudoti du modeliai. Pradžioje nagrinėjamos periodinės ilgosios linijos savybės, vėliau taikomas spiralinės sistemos modelis. Modelių analizė atliekama klasikiniu, matriciniu ir daugialaidžių linijų metodais. Taikomas kompiuterinis modeliavimas. Sudarytos įėjimo varžos, perdavimo ir lėtinimo koeficientų, vėlinimo laikų bei pereinamosios charakteristikos skaičiavimo programos. Parodyta, kad linijos su periodiniais netolygumais įgyja užtvarinio filtro savybes, kurios ryškėja, didėjant sistemos nevienalytiškumui. / In order to reveal general properties of the structures, containing periodical inhomogeneities, the inhomogeneous electromagnetic line and the inhomogeneous helical retard structure are considered. The overview of periodical systems and methods of their analysis are presented. The structures, containing periodical inhomogeneities, are analyzed using classical, matrix and multiconductor line methods. The programs for calculation of line input impedance, transfer coefficient, delay coefficient and width of the stop-band are developed. The results show that the stop–band appears due to periodical inhomogeneities and the width of the stop-band and the attenuation in it depend on intensities of periodical inhomogeneities.

L'auto-assemblage dynamique est une méthode puissante pour accéder à des édifices moléculaires fonctionnels complexes. Son application à la construction de moteurs moléculaires par le biais de la maîtrise des échelles de temps ouvre la voie à des générations de nano-machines de plus en plus sophistiquées pouvant spontanément renouveler leurs composants ou les changer pour d'autres. La première partie de ce manuscrit est axée sur le design d’hélices d’oligoamides aromatiques qui peuvent s’enrouler le long d’un axe et glisser rapidement le long de celui-ci avant de se dérouler. Le second volet de cette thèse est consacré à la mise en évidence d’un mouvement qui est caractérisé pour la première fois à l’échelle moléculaire: le vissage. Le dernier axe de recherche développé dans ce manuscrit concerne la mise en évidence d’un intermédiaire cinétique de type foldaxane se transformant progressivement en un complexe hôte-invité 2:2 thermodynamiquement stable. / Dynamic self-assembly is a powerful method for fabricating complex, functional molecular structures. Its application to the construction of molecular motors through the control of timescales paves the way for new generations of nano-machines, in which sophisticated components can be spontaneously renewed or changed by others. The first part of this thesis focuses on the design of aromatic oligoamides that can slowly wind along an axis and shuttle along it before unfolding. The second chapter is devoted to the detection of a movement that is characterized for the first time at the molecular level: the screwing motion. The last line of research developed in this manuscript concerns the identification of a long-lived kinetic supramolecular by-product based on foldaxane architecture, which gradually transforms into a thermodynamically favored 2:2 host-guest complex.

Les foldamères de type oligopyridine biscarboxamide constituent une famille d’oligomères synthétiques pouvant adopter une structure hélicoïdale et s’hybrider pour former des hélices doubles. Ce travail a eu pour objectif de synthétiser une nouvelle génération de foldamères π-fonctionnels porteurs de groupements photoactifs ou électroactifs, d’étudier les facteurs gouvernant l’équilibre entre hélice simple et hélice double, d’analyser l’impact de cet équilibre sur les propriétés optiques, et enfin de mettre en place un nouveau type de stimulus permettant de contrôler cet équilibre. Deux foldamères photoactifs dotés d’unités Disperse Red, ont été synthétisés. Leurs structures cristallographiques confirment la formation de structures hélicoïdales. Un choix précis du solvant permet d’orienter sélectivement l’équilibre vers la formation d’une hélice simple ou double.Le contrôle de l’équilibre d’hybridation par dilution permet de moduler l’activité en Génération de Seconde Harmonique du foldamère. En outre, la cavité générée par l'hélice permet la reconnaissance de divers anions. Enfin, les premiers efforts fournis pour induire une hélicité donnée à ces foldamères par voie supramoléculaire sont décrits. Par ailleurs, un foldamère électroactif fonctionnalisé par deux unités tétrathiafulvalène (TTF) a été synthétisé selon une méthodologie originale. La présence des unités TTF permet un contrôle redox inédit de la structuration du foldamère, par dimérisation de cations radicaux. Le concept a été élargi via l’immobilisation d’un foldamère sur surface d’or (SAMs). Enfin, une capsule électroactive capable de complexer l’acide tartrique a également été synthétisée et caractérisée. / Oligopyridine biscarboxamide-based foldamers constitute a family of synthetic oligomers that can fold into helical structures and hybridize to form double helices. This work aims at synthesizing a new generation of π-functionalized foldamers featuring photoactive and electroactive moieties, in order: to study the factors governing the equilibrium between simple and double helices, to analyze the impact of this equilibrium on the optical and recognition properties, and to set up a new type of stimulus to control this equilibrium. Two photoactive foldamers of different lengths and bearing two Disperse Red units were synthesized. Their crystallographic structures confirm the formation of helical structures. A precise choice of the solvent allows to drive the equilibrium towards the single or the double helix selectively.The cavity generated within the helix presents a good affinity for anions. The control over the hybridization equilibrium allows modulating the Second Harmonic Generation activity. Eventually, our first efforts to control the helicity of these foldamers through supramolecular chiral induction are described. On the other hand, an electroactive foldamer featuring two tetrathiafulvalene (TTF) units was synthesized according to an original methodology. The presence of TTF units allows an unprecedented redox control of the structure of foldamer, by dimerization of radical cations. The concept has been extended by immobilizing a foldamère on a gold surface (SAMs). Finally, an electroactive capsule capable of complexing tartaric acid has also been synthesized and characterized.

In recent years, several interesting biological roles played by RNA have come to light. Apart from their known role in translation of genetic information from DNA to protein, they have been shown to act as enzymes as well as regulators of gene expression. Protein-RNA complexes are involved in regulating cellular processes like cell division, differentiation, growth, cell aging and death. A number of clinically important viruses have RNA as their genetic material. Defective RNA molecules have been linked to a number of human diseases. The ability of RNA to adopt stunningly complex three-dimensional structures aids in diverse functions like catalysis, metabolite sensing and transcriptional control. Several secondary structure motifs are observed in RNA, of which the double-helical RNA motif is ubiquitous and well characterized. Though DNA duplexes have been shown to be present in many polymorphic states, RNA duplexes are believed to exhibit conservatism. Early fibre diffraction analysis on molecular structures of natural and synthetically available oligo- and polynucleotides suggested that the double-helical structures of RNA might exist in two forms: A-form and A′-form. New improved crystallographic methods have contributed to the increased availability of atomic resolution structures of many biologically significant RNA molecules. With the available structural information, it is feasible to try and understand the contribution of the variations at the base pair, base-pair step and backbone torsion angle level to the overall structure of the RNA duplex. Further, the effect of protein binding on RNA structure has not been extensively analysed. These studies have not been investigated in greater detail due to the focus of the research community on understanding conformational changes in proteins when bound to RNA, and due to the lack of a significant number of solved RNA structures in both free and protein-bound state. While studies on the conformation of the DNA double-helical stem have moved beyond the dinucleotide step into tri-, tetra-, hexa- and octanucleotide levels, similar knowledge for RNA even at the dinucleotide step level is lacking. In this thesis, the results of detailed analyses to understand the contribution of the base sequence towards RNA conformational variability as well as the structural changes incurred upon protein binding are reported. Objectives The primary objective of this thesis is to understand the following through detailed analyses of all available high-resolution crystal structures of RNA. 1 Exploring sequence-dependent variations exhibited by dinucleotide steps formed by Watson-Crick (WC) base pairs in RNA duplexes. 2 Identifying sequence-dependent variations exhibited by dinucleotide steps containing non-Watson-Crick (NWC) base pairs in RNA duplexes. 3 Developing a web application for the generation of sequence-dependent non-uniform nucleic acid structures. 4 Investigating the relationship between base sequence and backbone torsion-angle preferences in RNA double helices followed by molecular dynamics simulation using various force fields, to check their ability to reproduce the above experimental findings. Chapter 1 gives an overview of the structural features and polymorphic states of RNA duplexes and the present understanding of the structural architecture of RNA, thereby laying the background to the studies carried out subsequently. The chapter also gives a brief description on the methodologies applied. Relevant methodologies and protocols are dealt with in detail in the respective chapters. Sequence-dependent base-pair step geometries in RNA duplexes A complete understanding of the conformational variability seen in duplex RNA molecules at the dinucleotide step level can aid in the understanding of their function. This work was carried out to derive geometric information using a non-redundant RNA crystal structure dataset and to understand the conformational features (base pair and base-pair step parameters) involving all Watson-Crick (WC) (Chapter 2) and non-Watson-Crick (NWC) base pairs (Chapter 3). The sequence-dependent variations exhibited by the base-pair steps in RNA duplexes are elaborated. Further, potential non-canonical hydrogen bond interactions in the steps are identified and their relationship with dinucleotide step geometry is discussed. Comparison of the features of dinucleotide steps between free and protein-bound RNA datasets suggest variations at the base-pair step level on protein binding, which are more pronounced in non-Watson-Crick base pair containing steps. Chapter 4 describes a web-server NUCGEN-Plus, developed for building and regeneration of curved and non-uniform DNA and RNA duplexes. The main algorithm is a modification of our earlier program NUCGEN that worked mainly for DNA. The WC step parameters and intra-base parameters for RNA were obtained from the work detailed in Chapter 2. The FORTRAN code and input sequence file format was modified. The program has two modules: a) Using the model-building module, the program can build duplex structures for a given input DNA/RNA sequence. Options are available for selecting various derived or user specified base-pair step parameters, and fibre diffraction parameters that can be used in the building process. The program can generate double-helical structures up to 2000 nucleotides in length. In addition, the program can calculate the curvature of the generated duplex at defined length scale. b) Using the regeneration module, double-helical structures of nucleic acids can be rebuilt from the existing solved structures. Further, variants of an existing structure can be generated by varying the input geometric parameters. The web-server has a user-friendly interface and is freely available in the public domain at: http://nucleix.mbu.iisc.ernet.in/nucgenplus/index.html Sequence dependence of backbone torsion angle conformers in RNA duplexes RNA molecules consist of covalently linked nucleotide units. Each of these units has six rigid torsional degrees of freedom (α, β, γ, δ, ε, and ζ) for the backbone and one (χ) around the glycosidic bond connecting the base to the ribose, thereby providing conformational flexibility. An understanding of the relationship between base sequence and structural variations along the backbone can help deduce the rationale for sequence conservation and also their functional importance. Chapter 5 describes in detail the torsion angle-dependent variations seen in dinucleotide steps of RNA duplex. A non-redundant, high resolution (≤2.5Å) crystal structure dataset was created. Base-specific preferences for the backbone and glycosidic torsion angles were observed. Non-A-form torsion angle conformers were found to have a greater prevalence in protein-bound duplexes. Further validation of the above observation was performed by analysing the RNA backbone conformers and the effect of protein binding, in the crystal structure of E. coli 70S ribosome. Chapter 5 further describes the molecular dynamics simulation studies carried out to understand the effect of force fields on the RNA backbone conformer preferences. A 33mer long duplex was simulated using seven different force fields available in AMBER and CHARMM program, each for 100 ns. Trajectory analyses suggest the presence of sequence-dependent torsion angle preferences. Torsion angle conformer distribution closer to that of crystal structures was observed in the system simulated using parmbsc0 force field. Molecular dynamics simulation studies of AU/AU base-pair step A unique geometric feature, unlike that in other purine-pyrimidine (RY) steps in the crystal dataset analysis, was reported for AU/AU step (see Chapter 2). Appendix 1 describes the work carried out to validate these features observed in the crystal structures using simulation studies. Additionally, the effect of nearest-neighbor base pairs on the AU/AU step geometry were examined. General Conclusion Overall, the findings of this thesis work suggest that RNA duplexes exhibit sequence-dependent structural variations and sample a large volume of the double-helical conformational space. Further, protein binding affects the local base-pair step geometry and backbone conformation.