Signal transduction with hybridization chain reactions

Some of the most exciting developments in the field of nucleic acid engineering include the utilization of synthetic nucleic acid molecular devices as gene regulators, as disease marker detectors, and most recently, as therapeutic agents. The common thread between these technologies is their reliance on the detection of specific nucleic acid input markers to generate some desirable output, such as a change in the copy number of an mRNA (for gene regulation), a change in the emitted light intensity (for some diagnostics), and a change in cell state within an organism (for therapeutics). The research presented in this thesis likewise focuses on engineering molecular tools that detect specific nucleic acid inputs, and respond with useful outputs.

Four contributions to the field of nucleic acid engineering are presented: (1) the construction of a single nucleotide polymorphism (SNP) detector based on the mechanism of hybridization chain reaction (HCR); (2) the utilization of a single-stranded oligonucleotide molecular Scavenger as a means of enhancing HCR selectivity; (3) the implementation of Quenched HCR, a technique that facilitates transduction of a nucleic acid chemical input into an optical (light) output, and (4) the engineering of conditional probes that function as sequence transducers, receiving target signal as input and providing a sequence of choice as output. These programmable molecular systems are conceptually well-suited for performing wash-free, highly selective rapid genotyping and expression profiling in vitro, in situ, and potentially in living cells.

Chain-forming zintl antimonides as novel thermoelectric materials

Zintl phases, a subset of intermetallic compounds characterized by covalently-bonded "sub-structures," surrounded by highly electropositive cations, exhibit precisely the characteristics desired for thermoelectric applications. The requirement that Zintl compounds satisfy the valence of anions through the formation of covalent substructures leads to many unique, complex crystal structures. Such complexity often leads to exceptionally low lattice thermal conductivity due to the containment of heat in low velocity optical modes in the phonon dispersion. To date, excellent thermoelectric properties have been demonstrated in several Zintl compounds. However, compared with the large number of known Zintl phases, very few have been investigated as thermoelectric materials.

From this pool of uninvestigated compounds, we selected a class of Zintl antimonides that share a common structural motif: anionic moieties resembling infinite chains of linked MSb₄ tetrahedra, where $M$ is a triel element. The compounds discussed in this thesis (A₅M₂Sb₆ and A₃MSb₃, where A = Ca or Sr and M = Al, Ga and In) crystallize as four distinct, but closely related "chain-forming" structure types. This thesis describes the thermoelectric characterization and optimization of these phases, and explores the influence of their chemistry and structure on the thermal and electronic transport properties. Due to their large unit cells, each compound exhibits exceptionally low lattice thermal conductivity (0.4 - 0.6 W/mK at 1000 K), approaching the predicted glassy minimum at high temperatures. A combination of Density Functional calculations and classical transport models were used to explain the experimentally observed electronic transport properties of each compound. Consistent with the Zintl electron counting formalism, A₅M₂Sb₆ and A₃MSb₃ phases were found to have filled valence bands and exhibit intrinsic electronic properties. Doping with divalent transition metals (Zn²⁺ and Mn²⁺) on the M³⁺ site, or Na¹⁺ on the A³⁺ site allowed for rational control of the carrier concentration and a transition towards degenerate semiconducting behavior. In optimally-doped samples, promising peak zT values between 0.4 and 0.9 were obtained, highlighting the value of continued investigations of complex Zintl phases.

Intramolecular conflict : conformation and self-assembly of architecturally complex macromolecules in solution

The solution behavior of linear polymer chains is well understood, having been the subject of intense study throughout the previous century. As plastics have become ubiquitous in everyday life, polymer science has grown into a major field of study. The conformation of a polymer in solution depends on the molecular architecture and its interactions with the surroundings. Developments in synthetic techniques have led to the creation of precision-tailored polymeric materials with varied topologies and functionalities. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer architecture and their conformation and behavior. To meet that need, this thesis investigates the conformation and self-assembly of three architecturally complex macromolecular systems with rich and varied behaviors driven by the resolution of intramolecular conflicts. First we describe the development of a robust and facile synthetic approach to reproducible bottlebrush polymers (Chapter 2). The method was used to produce homologous series of bottlebrush polymers with polynorbornene backbones, which revealed the effect of side-chain and backbone length on the overall conformation in both good and theta solvent conditions (Chapter 3). The side-chain conformation was obtained from a series of SANS experiments and determined to be indistinguishable from the behavior of free linear polymer chains. Using deuterium-labeled bottlebrushes, we were able for the first time to directly observe the backbone conformation of a bottlebrush polymer which showed self-avoiding walk behavior. Secondly, a series of SANS experiments was conducted on a homologous series of Side Group Liquid Crystalline Polymers (SGLCPs) in a perdeuterated small molecule liquid crystal (5CB). Monodomain, aligned, dilute samples of SGLCP-b-PS block copolymers were seen to self-assemble into complex micellar structures with mutually orthogonally oriented anisotropies at different length scales (Chapter 4). Finally, we present the results from the first scattering experiments on a set of fuel-soluble, associating telechelic polymers. We observed the formation of supramolecular aggregates in dilute (≤0.5wt%) solutions of telechelic polymers and determined that the choice of solvent has a significant effect on the strength of association and the size of the supramolecules (Chapter 5). A method was developed for the direct estimation of supramolecular aggregation number from SANS data. The insight into structure-property relationships obtained from this work will enable the more targeted development of these molecular architectures for their respective applications.

Synthesis and characterization of high-spin organic materials: prototypes for the polaronic ferromagnet

The design, synthesis and magnetic characterization of thiophene-based models for the polaronic ferromagnet are described. Synthetic strategies employing Wittig and Suzuki coupling were employed to produce polymers with extended π-systems. Oxidative doping using AsF_5 or I_2 produces radical cations (polarons) that are stable at room temperature. Magnetic characterization of the doped polymers, using SQUID-based magnetometry, indicates that in several instances ferromagnetic coupling of polarons occurs along the polymer chain. An investigation of the influence of polaron stability and delocalization on the magnitude of ferromagnetic coupling is pursued. A lower limit for mild, solution phase I_2 doping is established. A comparison of the variable temperature data of various polymers reveals that deleterious antiferromagnetic interactions are relatively insensitive to spin concentration, doping protocols or spin state. Comparison of the various polymers reveals useful design principles and suggests new directions for the development of magnetic organic materials. Novel strategies for solubilizing neutral polymeric materials in polar solvents are investigated.

The incorporation of stable bipyridinium spin-containing units into a polymeric high-spin array is explored. Preliminary results suggest that substituted diquat derivatives may serve as stable spin-containing units for the polaronic ferromagnet and are amenable to electrochemical doping. Synthetic efforts to prepare high-spin polymeric materials using viologens as a spin source have been unsuccessful.

Value chain analysis for sea cucumber in the Philippines

This study examined the sea cucumber industry in the Philippines through the value chain lens. The intent was to identify effective pathways for the successful introduction of sandfish culture as livelihood support for coastal communities. Value chain analysis is a high-resolution analytical tool that enables industry examination at a detailed level. Previous industry assessments have provided a general picture of the sea cucumber industry in the country. The present study builds on the earlier work and supplies additional details for a better understanding of the industry's status and problems, especially their implications for the Australian Center for International Agricultural Research (ACIAR) funded sandfish project "Culture of sandfish (Holothuria scabra) in Asia- Pacific" (FIS/2003/059). (PDF contains 54 pages)

Estudo da influência do teor de segmentos hidrofílicos na síntese de poliuretanos dispersos em água

Considerações ambientais têm aumentado a pesquisa e o desenvolvimento de sistemas poliméricos aquosos para diversos tipos de aplicações, principalmente como revestimentos. Nesta dissertação, foram sintetizadas formulações não-poluentes à base de poliuretanos dispersos em água (PUDs), com 40% de teor de sólidos, na ausência de solventes orgânicos. Os monômeros empregados foram copolímeros em bloco à base de poli(glicol etilênico) e poli(glicol propilênico) (EG-b-PG), com teor de 25% de segmento hidrofílico EG, poli (glicol propilênico) (PPG), ácido dimetilolpropiônico (DMPA), diisocianato de isoforona (IPDI) e hidrazina (HYD), como extensor de cadeia. Foram variadas as razões entre o número de equivalente-grama de grupamentos isocianato e hidroxila (NCO/OH) e a proporção em equivalente-grama de PPG e dos copolímeros em bloco (EG-b-PG). Foi observado que a incorporação de altas quantidades de copolímero dificultou a síntese dos poliuretanos dispersos em água, levando à formação de géis. O tamanho médio de partícula e a viscosidade das dispersões foram determinados. Os filmes vazados a partir dessas dispersões foram avaliados quanto à capacidade de absorção de água, resistência mecânica, termogravimetria (TG), e caracterizados por espectroscopia na região do infravermelho (FTIR). As dispersões poliuretânicas produzidas se mostraram satisfatórias quando aplicadas como revestimento para madeira, metais e vidro

Fixação de complexo de ferro II em matriz de poli(acrilato de sódio)

Neste trabalho estudou-se a complexação do poli(acrilato de sódio), PAS, com aminpentacianoferrato de sódio,APCF. As reações de complexação ocorreram imediatamente com a formação de uma coloração amarela com total solubilização do polímero na solução 0,032 M molar do complexo. As soluções mostraram-se estáveis por 48 h e após esse período observou-se alterações na natureza do complexo polimérico com a formação de precipitado. O UV foi usado como ferramenta de caracterização do complexo. O máximo de absorção obtido após dissolução imediata foi de 405 nm com desvio para o azul (398 nm) e um pequeno efeito hipercrômico. As amostras mantidas à temperatura ambiente por mais de 48 h deram origem a precipitados, que como a solução, absorveram com máximo de 364, 389 e 398 nm. O Complexo PAS-APCF foi também caracterizado através de FTIR por ATR e apresentou pequenas variações no espectro do material de partida (PAS). Um incremento na intensidade da deformação axial assimétrica do grupo carboxilato (1651 cm-1) e a presença do estiramento em 2055 cm-1 do grupo cianeto, diferentemente do APCF (2048 cm-1), confirmaram a formação do complexo PAS-APCF. As freqüências de absorção observadas para o complexo foram compatíveis com a presença de estruturas mono e bidentadas de complexação. As análises de TGA e DSC também foram utilizadas para a caracterização das estruturas. O estudo modelo envolvendo a complexação de sais sódicos de diácidos orgânicos de diferentes tamanhos de cadeia (oxalato, malonato, succinato, glutarato e adipato), diferentemente do PAS, promoveu um desvio para o vermelho na frequência máxima de absorção junto de um pequeno efeito hipercrômico (421 nm). Esta variação pode também ser observada quando do emprego de acetato de sódio, indicando, provavelmente, apenas a formação de estruturas monodentadas