The RNA World hypothesis suggests that RNA, or a proto-RNA, existed in an early form of life that had not yet developed the ability to synthesize protein enzymes. This hypothesis, by some interpretations, implies that nucleic acid polymers were the first polymers of life, and must have therefore spontaneously formed from simple molecular building blocks in the "prebiotic soup." Although prebiotic chemists have searched for decades for a process by which RNA can be made from plausible prebiotic reactions, numerous problems persist that stand in the way of a chemically-sound model for the spontaneous generation of an RNA World (e.g., strand-cyclization, heterogeneous backbones, non-selective ligation of activated nucleotides). The Molecular Midwife hypothesis, proposed by Hud and Anet in 2000, provides a possible solution to several problems associated with the assembly of the first nucleic acids. In this hypothesis, nucleic acid base pairs are assembled by small, planar molecules that resemble molecules which are known today to intercalate the base pairs of nucleic acid duplexes. Thus, the validity and merits of the Molecular Midwife hypothesis can be, to some extent, explored by studying the effects of intercalation on the non-covalent assembly of nucleic acids. In this thesis, I explore the role of the sugar-phosphate backbone in dictating the structure and thermodynamics of nucleic acid intercalation by using 2′,5′-linked RNA intercalation as a model system of non-natural nucleic acid intercalation. The solution structure of an intercalator-bound 2′,5′ RNA duplex reveals structural and thermodynamic aspects of intercalation that provide insight into the origin of the nearest-neighbor exclusion principle, a principle that is uniformly obeyed upon the intercalation of natural (i.e. 3′,5′-linked) RNA and DNA. I also demonstrate the ability of intercalator-mediated assembly to circumvent the strand-cyclization problem, a problem that otherwise greatly limits the polymerization of short oligonucleotides into long polymers. Together, the data presented in this thesis illustrate the important role that the nucleic acid backbone plays in governing the thermodynamics of intercalation, and provide support for the proposed role of intercalator-mediated assembly in the prebiotic formation of nucleic acids.

In the past 30 years, the discovery of capabilities of nucleic acids far beyond their well-known information-bearing capacity has profoundly influenced our understanding of these polymers. The discovery by the Cech and Altman labs that nucleic acids could perform catalytic functions, coupled with the Gold and Szostak groups’ demonstration of the de novo evolution of nucleic acids that bind arbitrary ligands, has resulted in a proliferation of newfound roles for these molecules. Nucleic acids have found utility in both engineered systems, such as aptamer therapeutics, as well as in newly appreciated roles in extant organisms, such as riboswitches. As a result of these discoveries, many have pondered the potential importance of the dual (catalytic and informational) roles of nucleic acids in early evolution. A high-yielding synthetic route for the nonenzymatic polymerization of nucleic acids, based on the aqueous self-assembly of their components, would provide a powerful tool in nucleic acid chemistry, with potential utility in prebiotic and contemporary nucleic acid systems alike – however, such a route remains elusive. In this thesis, I describe several steps towards such a synthetic route. In these systems, a nucleic-acid binding ligand drives the assembly of short DNA and RNA duplexes, promoting the production of long nucleic acid polymers, while suppressing the production of short, cyclic species. Additionally, the use of a reversible covalent linkage allows for the production of long polymers, as well as the incorporation of previously cyclized products into these polymers. I also report several explorations of novel base pairings, nucleic acid-ligand interactions, and nucleic acid-ion interactions that have informed our studies of self-assembling nucleic acid systems.

Orientador: Prof. Dr. Wagner Alves Carvalho / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós-Graduação em Ciência e Tecnologia/Química, 2016. / Zeólitas hierárquicas possuindo estrutura tipo MFI foram preparadas hidrotermicamente utilizando surfactantes como agentes direcionadores de estrutura, constituídos por grupos de amônio quaternário sintetizados neste trabalho. A zeólita preparada utilizando o agente polimérico apresentou uma morfologia tipo nanoesponja com poros de diâmetro elevado. Utilizando o agente direcionador de estrutura C22-6-6 com adição de agente nucleante originou uma zeólita de morfologia tipo nanoesponja, composta por uma rede desordenada tridimensional de camadas MFI com espessura de 2,5nm suportando umas as outras. Com o mesmo agente direcionar, preparou-se uma zeólita de morfologia unilamelar e um material sem adição de alumínio, denominado nanossilicato. Este último material foi submetido a três métodos pós-síntese para modificação da superfície, visando o aumento de acidez. O desempenho catalítico das zeólitas MFI hierárquica e convencional foi investigado na eterificação de glicerol com álcool terc-butílico em fase líquida e na desidratação da frutose em várias condições: fase aquosa, fase orgânica e extração in situ da fase aquosa. As zeólitas hierárquicas foram mais ativas do que as amostras microporosas em ambas as reações, o que pode ser atribuído aos sítios ácidos localizados nas superfícies externas, acessíveis para os reagentes volumosos. A maior seletividade para 5-hidroximetilfurfural foi obtida com nanossilicatos modificados utilizando extração in situ. / Hierarchical zeolites possessing MFI framework type were hydrothermally prepared using surfactants as structure-directing agents consisting of quaternary ammonium groups prepared in this work. The zeolite prepared using polymeric structure-directing agent presented a nanosponge-like morphology with larger pores. The structure-directing agent C22-6-6 was used to prepare materials with different morphologies. Using the seed-assisted synthesis method, a nanosponge-like morphology was obtained. This zeolite was composed of a three-dimensional disordered network of MFI layers with 2.5nm thickness supporting each other. Furthermore, a unilamelar nanosheet zeolite was also prepared, as well as a material without aluminum, called nanosilicate. This last one was submitted to three post synthesis methods for surface modification in order to increase acidity. Catalytic performance of the MFI zeolites, both hierarchical and conventional, was investigated in glycerol etherification with tert-butyl alcohol in liquid phase, and in fructose dehydration in various conditions: aquous phase, organic phase and in situ extraction. Hierarchical zeolites were more active than conventional samples in both reactions, which can be attributed to the acid sites located on the external surfaces accessible for the reaction of bulky reactants. The highest selectivity to 5-hydroxymethyfurfural were obtained with modified nanosilicates and in in situ extraction.

<p>Nanotechnology has experienced a tremendous rise in the last decade. The synthesis of nanomaterials of defined structure and controlled properties is one of the most challenging part. Solution processing bottom-up fabrication techniques enables the facile synthesis of low dimension and ordered structures with low cost through the self-assembly of basic building blocks. Biotemplating has become an emerging field in which natural biomolecular objects are utilized for creating functional, hierarchical, controlled patterned structures with nanometric precision. It is a capital effective, eco-friendly and energy-efficient synthetic process. Viral biotemplating has shown great potential in electronics, environmental and biomedical devices. In recent years, in-planta produced Tobacco Mosaic Virus (TMV) and its variants have been used to produce metal nanorods and nanowires of monodisperse structures under mild conditions without the use of harsh chemical treatments although there remains much to be understood. Mass production of biotemplate, programming of viral particles of desired functionalities, manipulation for biomineralized metal materials of good quality have not been sufficiently studied to allow for directed synthesis. The fundamental studies on platform development for viral biotemplate production, design of viral proteins carrying engineered properties, and the hydrothermal synthesis of biotemplated metal nanomaterials, which create great uniformity and high coverage are of interest in this dissertation. Three experimental studies are outlined.<br></p><p><br></p><p>A novel virus biotemplate, Barley stripe mosaic virus (BSMV) virus-like particle is designed and engineered through genetic engineering. By fusing the Origin of Assembly from TMV to the transcript encoding BSMV capsid protein, the self-assembly of BSMV-VLP nanorod from microbial-based protein expression system was achieved for the first time. An alternate platform for viral particle production has been developed. Optimization of VLP expression, purification and processing conditions are performed. This developed alternative E. coli production platforms offer unique opportunities for genetic engineering and faster protein expression; therefore, the development of our system enables rapid design-build-test cycles for the engineering and production of BSMV-VLPs with desired properties. Results in this project shows the power of genetic engineering and serves as a springboard for genetic engineering of the VLPs.<br></p><p><br></p><p>Programming on BSMV-VLP is further used to decouple the VLP assembly into governing internal molecular interactions. To drive the nucleic acid free helical BSMV-VLP rod assembly and further increase the stability of capsid proteins, an identification of Caspar Carboxylate cluster in BSMV is performed. Various carboxylate residues were selected through protein crystal structure and examined systematically through experimental work. By introducing mutations on selected residues, the intersubunit carboxylate interaction of the proteins was significantly altered, resulting in an in vivo production of nucleic-acid free BSMV-VLP assembly for the first time. The change in interactions leads to increased stability of the modified VLP, enabling the formation of longer nanorods with lengths over one micrometer. Moreover, both wild-type and mutated BSMV-VLPs were shown to have great structural stability across a wide range of pHs. Overall, we exhibit experimental identification to systematically probe the key carboxylate interactions to increase the stability of proteins and drive RNA-free BSMV-VLP assembly. This project greatly expands the potential usefulness of the engineered BSMV-VLP biotemplates for a wide variety of applications.<br></p><p><br></p><p>Finally, to demonstrate the versatile uses of BSMV-VLP in biotemplating, the new biotemplate was utilized to expand understandings on the directed synthesis of metal nanostructures. By using the hydrothermal synthesis, VLPs were successfully utilized to synthesize monometallic palladium nanorods with a wide range of length scales. The VLP-mediated nanorods are more uniformly and fully-covered than the ones synthesized with in planta-produced BSMV virion. Besides, the synthesis shows an effective control over the metal nanorod diameter. The capability of BSMV-VLP was readily expanded from the synthesis of monometallic nanorods to bimetallic hybrid. In the absence of an exogenous reducing agent, mineralization of platinum, gold and copper was successfully demonstrated on the VLP. It is attributed to lower reduction barrier introduced by already-deposited palladium nanoparticles which serve as nucleation sites for subsequent metal reduction. The formation of bimetallic complexes was further supported by STEM, EDS and XPS analysis evidenced the presences of multiple metals. Overall, BSMV-VLP-mediated biotemplating using the hydrothermal synthesis has been confirmed to be a promising and feasible approach to create organic-inorganic complex nanocomposite.<br></p><p><br></p><p>Lastly, to move toward an application, the synthesized Pd nanorods coated with full coverage and great uniformity of nanoparticles were utilized as an exciting hydrogen sensing material. The developed hydrogen sensing system using a quartz crystal microbalance shows a fast response toward hydrogen as well as the ability of hydrogen detection and quantification of the adsorption capacity. This study serves as an entry point and opens up enormous possibility for next-generation of Pd-virus hybrid hydrogen sensors.<br></p><p><br></p><p>Taken together, this dissertation has demonstrated the engineering and production of a novel BSMV virus-like particle bacterial system. This alternative platform and developed parameter space for VLP production is genetically tractable and requires significantly shorter processing duration for large-scale and mass production. The BSMV-VLP biotemplated metal nanomaterials present great qualities and controllable dimensions. This approach has explored the synthetic palette and opened up enormous possibilities in the bottom-up nanofabrication of versatile and tunable organic-inorganic nanoscaled complex and would facilitate future engineering industrial applications.<br></p>

This thesis describes supramolecular approaches to porphyrin nanorings. Cyclic porphyrin arrays resemble natural light harvesting systems, and it is of interest to probe the photophysical effects of bending the porphyrin aromatic π-system. A general overview of the synthesis and photophysical properties of porphyrins and their arrays is carried out in Chapter 1. The electronic structure of porphyrins is examined, and how conformational effects in oligomers, such as inter-porphyrin torsional angle and backbone bending influence the π-conjugation pathway. The structures of light harvesting complexes are discussed. Chapter 2 describes the design and synthesis of a complementary 12-armed template designed to coordinate linear porphyrin oligomers in the correct conformation for cyclisation to give a cyclic porphyrin dodecamer. Chapter 3 demonstrates two approaches to a cyclic porphyrin dodecamer ring. Firstly, a classical templating approach using the 12-armed template is described. The limitations of this approach in the quest for larger nanorings are discussed. Vernier templating, which utilises a mismatch in the number of binding sites between a ligand and its receptor is introduced as a general strategy to the synthesis of large nanorings. This is demonstrated by the synthesis of cyclic dodecamer from a linear porphyrin tetramer and a hexadentate template via a figure-of-eight intermediate. The general utility of the Vernier method to large nanorings is explored in Chapter 4 with steps towards the synthesis of a cyclic tetracosamer, consisting of 24 porphyrin subunits. In preliminary experiments, an improved route to the cyclic porphyrin octamer is described. Finally, the photophysical properties of the nanoring series are explored in Chapter 5 as a function of size and conformation. Femtosecond photoluminescence spectroscopy shows that even in cyclic dodecamer, exciton delocalisation over the entire porphyrin backbone occurs on a sub-picosecond timescale, and parallels are drawn with the dynamics of natural light harvesting complexes.