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This dissertation focuses on rationalised DNA design as a tool for the discovery and development of new therapeutic entities, as well as understanding the biological function of DNA beyond the storage of genetic information. The study is comprised of two main areas of study: (i) the use of DNA as a coding unit to illustrate the relationship between code-diversity and dynamics of self-assembly; and (ii) the use of DNA as an active unit that interacts and regulates a target protein. In the study of DNA as a coding unit in code-diversity and dynamics of self-assembly, we developed the DNA-Based Diversity Modelling and Analysis (DDMA) method. Using Polymerase Chain Reaction (PCR) and Real Time Polymerase Chain Reaction (RT-PCR), we studied the diversity and evolution of synthetic oligonucleotide populations. The manipulation of critical conditions, with monitoring and interpretation of their effects, lead to understanding how PCR amplification unfolding could reshape a population. This new take on an old technology has great value for the study of: (a) code-diversity, convenient in a DNA-based selection method, so semi-quantitation can evaluate a selection development and the population\'s behaviour can indicate the quality; (b) self-assembly dynamics, for the simulation of a real evolution, emulating a society where selective pressures direct the population's adaptation; and (c) development of high-entropy DNA structures, in order to understand how similar unspecific DNA structures are formed in certain pathologies, such as in auto-immune diseases. To explore DNA as an active unit in Tumour Necrosis Factor α (TNF-α) interaction and activity modulation, we investigate DNA's influence on its spatial conformation by physical environment regulation. Active TNF-α is a trimer and the protein-protein interactions between its monomers are a promising target for drug development. It has been hypothesised that TNF-α forms a very intricate network after its activation between its subunits and receptors, but the mechanism is still not completely clear. During our research, we estimate the non-specific DNA binding to TNF-α in the low micro-molar range. Cell toxicity assays confirm this interaction, where DNA consistently enhances TNF-α's cytotoxic effect. Further binding and structural studies lead to the same conclusion that DNA binds and interferes with TNF-α structure. From this protein-DNA interaction study, a new set of tools to regulate TNF-α's biological activity can be developed and its own biology can be unveiled.

DNA-basierte Systeme beschreiben formal ein alternatives Berechnungskonzept, beruhend auf der Anwendung molekularbiologischer Operationen. Der Grundgedanke ist dabei die Entwicklung alternativer und universeller Rechnerarchitekturen. Infolge der zugrunde liegenden maximalen Parallelität sowie der hohen Komplexität entsprechender Systeme ist die Korrektheit jedoch schwer zu beweisen. Um dies zu ermöglichen werden in der Arbeit zunächst für drei verschiedene Systemklassen mit unterschiedlichen Berechnungsparadigmen strukturelle operationelle Semantiken definiert und bekannte Formalismen der Prozesstheorie adaptiert. Nachfolgend werden Tableaubeweissysteme beschrieben, mithilfe derer einerseits Invarianten und andererseits die jeweilige Korrektheit von DNA-basierten Systemen mit universeller Berechnungsstärke bewiesen werden können. Durch Anwendung dieser Konzepte konnte für drei universelle Systeme die Korrektheit gezeigt und für ein System widerlegt werden.

DNA-basierte Systeme beschreiben formal ein alternatives Berechnungskonzept, beruhend auf der Anwendung molekularbiologischer Operationen. Der Grundgedanke ist dabei die Entwicklung alternativer und universeller Rechnerarchitekturen. Infolge der zugrunde liegenden maximalen Parallelität sowie der hohen Komplexität entsprechender Systeme ist die Korrektheit jedoch schwer zu beweisen. Um dies zu ermöglichen werden in der Arbeit zunächst für drei verschiedene Systemklassen mit unterschiedlichen Berechnungsparadigmen strukturelle operationelle Semantiken definiert und bekannte Formalismen der Prozesstheorie adaptiert. Nachfolgend werden Tableaubeweissysteme beschrieben, mithilfe derer einerseits Invarianten und andererseits die jeweilige Korrektheit von DNA-basierten Systemen mit universeller Berechnungsstärke bewiesen werden können. Durch Anwendung dieser Konzepte konnte für drei universelle Systeme die Korrektheit gezeigt und für ein System widerlegt werden.

DNA nanotechnology has been developed in order to construct nanostructures and nanomachines by virtue of the programmable self-assembly properties of DNA molecules. Although DNA nanotechnology initially focused on spatial arrangement of DNA strands, new horizons have been explored owing to the development of the toehold-mediated strand-displacement reaction, conferring new dynamic properties to previously static and rigid structures. A large variety of DNA reconfigurable nanostructures, stepped and autonomous nanomachines and circuits have been operated using the strand-displacement reaction. Biological systems rely on information processing to guide their behaviour and functions. Molecular computation is a branch of DNA nanotechnology that aims to construct and operate programmable computing devices made out of DNA that could interact in a biological context. Similar to conventional computers, the computational processes involved are based on Boolean logic, a propositional language that describes statements as being true or false while connecting them with logic operators. Numerous logic gates and circuits have been built with DNA that demonstrate information processing at the molecular level. However, development of new systems is called for in order to perform new tasks of higher computational complexity and enhanced reliability. The contribution of secondary structure to the vulnerability of a toehold-sequestered device to undesired triggering of inputs was examined, giving new approaches for minimizing leakage of DNA devices. This device was then integrated as a logic component in a DNA-based computer with a retrievable memory, thus implementing two essential biological functions in one synthetic device. Additionally, G-quadruplex logic gates were developed that can be switched between two topological states in a logic fashion. Their individual responses were detected simultaneously, establishing a new approach for parallel biological computing. A new AND-NOT logic circuit based on the seesaw mechanism was constructed that, in combination with the already existing AND and OR gates, form a now complete basis set that could perform any Boolean computation. This work introduces a new mode of kinetic control over the operation of such DNA circuits. Finally, the first example of a transmembrane logic gate being operated at the single-molecule level is described. This could be used as a potential platform for biosensing.

<p>Self-assembly is a pervasive natural phenomenon that gives rise to complex structures and functions. It describes processes in which a disordered system of components form organized structures as a consequence of specific, local interactions among the components themselves, without any external direction. Biological self-assembled systems, evolved over billions of years, are more intricate, more energy efficient and more functional than anything researchers have currently achieved at the nanoscale. A challenge for human designed physical self-assembled systems is to catch up with mother nature. I argue through examples that DNA is an apt material to meet this challenge. This work presents:</p><p>1. 3D self-assembled DNA nanostructures.</p><p>2. Illustrations of the simplicity and power of toehold-mediated strand displacement interactions.</p><p>3. Algorithmic constructs in the tile assembly model.</p> / Dissertation

Forbidding and enforcing systems (fe-systems) provide a new way of defining classes of structures based on boundary conditions. Forbidding and enforcing systems on formal languages were inspired by molecular reactions and DNA computing. Initially, they were used to define new classes of languages (fe-families) based on forbidden subwords and enforced words. This paper considers a metric on languages and proves that the metric space obtained is homeomorphic to the Cantor space. This work studies Chomsky classes of families as subspaces and shows they are neither closed nor open. The paper investigates the fe-families as subspaces and proves the necessary and sufficient conditions for the fe-families to be open. Consequently, this proves that fe-systems define classes of languages different than Chomsky hierarchy. This work shows a characterization of continuous functions through fe-systems and includes results about homomorphic images of fe-families. This paper introduces a new notion of connecting graphs and a new way to study classes of graphs. Forbidding-enforcing systems on graphs define classes of graphs based on forbidden subgraphs and enforced subgraphs. Using fe-systems, the paper characterizes known classes of graphs, such as paths, cycles, trees, complete graphs and k-regular graphs. Several normal forms for forbidding and enforced sets are stated and proved. This work introduces the notion of forbidding and enforcing to posets where fe-systems are used to define families of subsets of a given poset, which in some sense generalizes language fe-systems. Poset fe-systems are, also, used to define a single subset of elements satisfying the forbidding and enforcing constraints. The latter generalizes graph fe-systems to an extent, but defines new classes of structures based on weak enforcing. Some properties of poset fe-systems are investigated. A series of normal forms for forbidding and enforcing sets is presented. This work ends with examples illustrating the computational potential of fe-systems. The process of cutting DNA by an enzyme and ligating is modeled in the setting of language fe-systems. The potential for use of fe-systems in information processing is illustrated by defining the solutions to the k-colorability problem.

Lindenmayer (L) systems form a class of interesting computational formalisms due to their parallel nature, the various circumstances under which they operate, the restrictions imposed on language acceptance, and other attributes. These systems have been extensively studied in the Formal Languages literature. In the past decade a new type of Lindenmayer system had been proposed: Watson-Crick Lindenmayer Systems. These systems are essentially a marriage between Developmental systems and DNA Computing. At their heart they are Lindenmayer systems augmented with a complementary relation amongst elements in the system just as the base pairs of DNA strands can be complementary with respect to one another. When conditions and a mechanism for 'switching' the state of a computation to it's complementary version are provided then these systems can become surprisingly more powerful than the L systems which form their backbone. This dissertation explores the computational power of new variants of Watson-Crick L systems. It is found that many of these systems are Computationally-Complete. These investigations differ from prior ones in that the systems under consideration have extended alphabets and usually Regular Triggers for complementation are considered as opposed to Context-Free Triggers investigated in previous works. / Thesis (Master, Computing) -- Queen's University, 2010-12-06 18:29:23.584

A área de biologia computacional está vivendo um crescimento rápido causado pela revolução no estudo de genômas e pelo avanço das técnicas de manipulação do material genético. Com essas novas tecnologias para manipulação de seqüências, a importância de achar uma solução eficiente para os problemas chamados de intratáveis também cresceu, pois muitos problemas envolvidos na análise de DNA pertencem a essa classe de problemas. Uma abordagem para achar essas soluções é usar o próprio DNA para realizar computação, aproveitando o paralelismo massivo utilizado em operações que manipulam seqüências de DNA. Isto é estudado na área de computação com DNA. Esse trabalho propõe um modelo formal para representar a estrutura da molécula de DNA e das operações que são realizadas com ela em laboratório. Este modelo ajuda a preencher a necessidade de uma descrição matemática que possa ser usada para analisar algoritmos baseados em DNA, assim como possibilitar a simulaç~o desses algoritmos em um computador. Foi utilizada a teoria de gramáticas de grafos, uma linguagem de especificação formal, para modelar as seqüências de DNA e suas I operações. O trabalho apresenta um estudo da estrutura da molécula de DNA, deScrevendo suas características e as principais operações que são realizadas para sua manipulação em laboratório. Uma descrição da teoria de Gramática de Grafos e sua aplicação também é apresentada. Para validação do modelo proposto as especificações resultantes foram adaptadas para o formato L-systems, outra linguagem de especificação formal, permitindo realizar a simulação da especificação no ambiente L-Studio. / The area of computational biology is living a fast growth, fed with a revolution in the study of genomes and with the advance in the techniques of genetic material manipulation. With these new technologies for manipulation of sequences, the relevance of finding efficient solution to the so-called computer intractable problems has also grown, because many problems involved in analyzing DNA belong to this class of problems. One approach to find such solutions is to use DNA itself to perform computations, taking advantage of the massive parallelism involved in operations that manipulate DNA sequences. This is what is studied in the area ofDNA computing. This work proposes a formal model to represent the DNA structure and the operations performed in laboratory with it. This model helps to fill the need of a mathematical description that can be used to analyze DNA-based algorithms, as well as for simulating such algorithms in a computer. We use graph grammars, a formal specification language, to model the DNA sequences and operations. The work presents a study of the DNA molecule structure, describing its features and the main operations performed for manipulation in laboratory. A description of the theory of Graph Grammars and its application are presented too. To validate the proposed model, the resulting DNA-graph grammar specifications are then translated into the L-systems format, another formal specification language, allowing for the simulation of the specifications using the L-Studio environment.

A computação com DNA é um campo da Bioinformática que, através da manipulação de seqüências de DNA, busca a solução de problemas. Em 1994, o matemático Leonard Adleman, utilizando operações biológicas e manipulação de seqüências de DNA, solucionou uma instância de um problema intratável pela computação convencional, estabelecendo assim, o início da computação com DNA. Desde então, uma série de problemas combinatoriais vem sendo solucionada através deste modelo de programação. Este trabalho analisa a computação com DNA, com o objetivo de traçar algumas linhas básicas para quem deseja programar nesse ambiente. Para isso, são apresentadas algumas vantagens e desvantagens da computação com DNA e, também, alguns de seus métodos de programação encontrados na literatura. Dentre os métodos estudados, o método de filtragem parece ser o mais promissor e, por isso, uma metodologia de programação, através deste método, é estabelecida. Para ilustrar o método de Filtragem Seqüencial, são mostrados alguns exemplos de problemas solucionados a partir deste método. / DNA computing is a field of Bioinformatics that, through the manipulation of DNA sequences, looks for the solution of problems. In 1994 the mathematician Leonard Adleman, using biological operations and DNA sequences manipulation, solved an instance of a problem considered as intractable by the conventional computation, thus establishing the beginning of the DNA computing. Since then, a series of combinatorial problems were solved through this model of programming. This work studies the DNA computing, aiming to present some basic guide lines for those people interested in this field. Advantages and disadvantages of the DNA computing are contrasted and some methods of programming found in literature are presented. Amongst the studied methods, the filtering method appears to be the most promising and for this reason it was chosen to establish a programming methodology. To illustrate the sequential filtering method, some examples of problems solved by this method are shown.