Improving the identification ability of surfaced-immobilized nucleic acid probes for small size DNA or RNA targets, utilizing optical or electrochemical methods, has been the goal for the gene chip technology. This study focuses on new probe design for introducing hairpin structural features and locked nucleic acid modification. We use three kinds of probes (DNA-LN, DNA-HP and LNA-HP) to prepare recognition layers via self-assembly processes on a gold substrate, and utilize AFM-based nanolithography technique to produce nanofeatures to observe the stiffness changes of oligonucleotide chains resulting from the formation of rigid double stranded duplexes when target sequence hybridizes to the probe. We also monitor the topographic changes upon exposure to the single mismatched and non-complementary targets as a function of time. The results reveal LNA-HP probes exhibit the highest response to discriminating single-point mutation in the base sequence. In addition, we study the effects of salt concentration, reaction temperature and the small size on the hybridization efficiency.

<p> DNA origami is a powerful method to construct DNA nanostructures. It requires long, single-stranded DNAs. The preparation of such long DNA strands is often quite tedious and has a limited production yield. In contrast, duplex DNAs can be easily prepared via enzymatic reactions in large quantities. Thus, we ask a question: can we design DNA nanostructures in such a way that the two complementary strands can simultaneously fold into the designed structures in the same solution instead of hybridizing with each other to form a DNA duplex? By engineering DNA interaction kinetics, herein, we are able to provide multiple examples to concretely demonstrate a positive answer to this question. The resulting DNA nanostructures have been thoroughly characterized by electrophoresis and atomic force microscopy imaging. The reported strategy is compatible with the DNA cloning method; thus, would provide a convenient way for large-scale production of the designed DNA nanostructures. </p>

No description available.

Bottom-up self-assembly has the potential to fabricate nanostructures with advanced electrical features. DNA templates have been used to enable such self-assembling methods due to their versatility and compatibility with various nanomaterials. This dissertation describes research to advance several different steps of biotemplated nanofabrication, from DNA assembly to characterization. I assembled different nanomaterials including surfactant-coated Au nanorods, DNA-linked Au nanorods and Pd nanoparticles on DNA nanotubes ~10 micrometer long, and on ~400 nm long bar-shaped DNA origami templates. I optimized seeding by changing the surfactant and magnesium ion concentrations in the seeding solution. After successful seeding, I performed electroless plating on those nanostructures to fabricate continuous nanowires. Using the four-point probe technique, I performed resistivity measurements for Au nanowires on DNA nanotubes and obtained values between 9.3 x 10-6 and 1.2 x 10-3 ohm meter. Finally, I demonstrated the directed placement of DNA origami using block copolymer self-assembly. I created a gold nanodot array using block copolymer patterning and metal evaporation followed by lift-off. Then, I used different ligand groups and DNA hybridization to attach DNA origami to the nanodots. The DNA hybridization approach showed greater DNA attachment to Au nanodots than localization by electrostatic interaction. These results represent vital progress in understanding DNA-templated components, nanomaterials, and block copolymer nanolithography. The work in this dissertation shows potential for creating DNA-templated nanodevices and their placement in an ordered array in future nanoelectronics. Each of the described materials and techniques further has potential for addressing the need for increased complexity and integration for future applications.

Algorithmic self-assembly has been an active area of research at the intersection of computer science, chemistry, and mathematics for almost two decades now, motivated by the natural self-assembly mechanism found in DNA and driven by the desire for precise control of nanoscale material manufacture and for the development of nanocomputing and nanorobotics. At the theoretical core of this research is the Abstract Tile Assembly Model (aTAM), the original abstract model of DNA tile self-assembly. Recent advancements in DNA nanotechnology have been made in developing strand displacement mechanisms that could allow DNA tiles to modify themselves during the assembly process by opening or closing certain binding sites, introducing new dynamics into tile self-assembly. We focus on one way of incorporating such signaling mechanisms for binding site activation and deactivation into the theoretical model of tile self-assembly by extending the aTAM to create the Active aTAM. We give appropriate definitions first for incorporating activation signals and then for incorporating deactivation signals and tile detachment into the aTAM. We then give a comparison of Active aTAM to related models, such as the STAM, and take a look at some theoretical results. The goal of the work presented here is to define and demonstrate the power of the Active aTAM with and without deactivation. To this end, we provide four constructions of temperature 1 (also known as "non-cooperative") active tile assembly systems that can simulate other computational systems. The first construction concerns the simulation of an arbitrary temperature 2 (also known as "cooperative") standard aTAM system in the sense of producing equivalent structures with a scaling factor of 2 in each dimension; the second construction generates the time history of a given 1D cellular automaton. The third and fourth constructions make use of tile detachment in order to dynamically simulate arbitrary 1D and 2D cellular automata with assemblies that record only the current state updates and not the entire computational history of the specified automaton.

<p>The manufacturing of molecular-scale computing systems requires a scalable, reliable, and economic approach to create highly interconnected, dense arrays of devices. As a candidate substrate for nanoscale logic circuits, DNA self-assembled nanostructures have the potential to fulfill these requirements. However, a number of open challenges remain, including the scalability of DNA self-assembly, long-range signal propagation, and precise patterning of functionalized components. These challenges motivate the development of theory and experimental techniques to illuminate the connections among the physical, optical, and thermodynamic properties of DNA self-assembled nanostructures. </p> <p>In this thesis, three tools are developed, validated, and applied to study the thermo-mechanical properties of DNA nanostructures: 1) a method to quantitatively measure the quality of DNA grid self-assembly, 2) a spectrofluorometer capable of capturing fluorescence and absorbance data under simultaneous multi-wavelength excitation, and 3) a Monte Carlo simulator that models the ensemble response of DNA nanostructures as simple harmonic oscillators. </p> <p>The broad contributions of this dissertation are as follows: 1) insight into the thermo-mechanical properties of DNA grid nanostructures, and 2) a categorization of self-assembly defects and their impact on proposed logic circuits. </p> <p>The results of the work presented in this dissertation show that: 1) the quality of self-assembly of DNA grid nanostructures can be quantitatively calculated to demonstrate the impact of changes in temperature or structure, 2) the optical absorbance of complex DNA nanostructures can be modeled to capture their thermo-mechanical properties (i.e., worst case within 10% of experimental melting temperatures and 70% of experimental thermodynamic parameters), 3) the structural resilience of DNA nanostructures can be quantifiably improved by chemical cross-linking with up to 60% retaining their original structure, and 4) DNA self-assembly introduces structural defects which create new fault models with respect to conventional technologies for logic circuits.</p> / Dissertation

<p>This dissertation hypothesizes,</p><p><italic>"It is possible to design a self-assembled, nanoscale, high-speed, resonance energy transfer device exhibiting non-linear gain with a few molecules."</italic></p><p>The report recognizes DNA self-assembly, a relatively inexpensive and a massively parallel fabrication process, as a strong candidate for self-assembled RET systems. It successfully investigates into the design and simulations of a novel sequential self-assembly process employed to realize the goal of creating large, scalable, fully-addressable DNA nanostructure-substrate for future molecular circuitry. </p><p>As a pre-cursor to the final device modeling various RET wire designs for interconnecting nanocircuits are presented and their modeling and simulation results are discussed. A chromophore RET system using a biomolecular sensor as a proof-of-concept argument that shows it is possible to model and characterize chromophore systems as a first step towards device modeling is also discussed. </p><p>Finally, the thesis report describes in detail the design, modeling, characterization, and fabrication of the Closed-Diffusive Exciton Valve: a self-assembled, nanoscale (area of 17.34 nm<super>2</super>), high-speed (3.5 ps to 6 ps) resonance energy transfer device exhibiting non-linear gain using only 10 molecules, thus confirming the hypothesis. It also recognized improvements that can be made in the future to facilitate better device operation and suggested various applications.</p> / Dissertation

Experiments have demonstrated that DNA molecules can compute like a machine to solve mathematical problems, which is significant because of their parallel computation ability. However, due to the nature of biochemical reactions, DNA computation suffers from errors, which are its main limitation. The abstract and kinetic Tile Assembly Models are now commonly used to simulate real DNA computing experiments, and to look for new methods to advance the accuracy of DNA-based computation. One means of controlling errors is through proofreading tile sets. Several such tile sets have been proposed in the literature, such as Chen and Goel’s snaked proofreading tile sets, the 2-way and 3-way overlay tile sets of Reif et al., and Rothemund and Cook’s n-way overlay tile sets. In the first part of this thesis, we analyze the performance of the Rothemund-Cook n-way overlay tile sets. We prove that the n-way overlay tile set contains n^2+3n+4 rule tiles. Simulation results show that these tile sets clearly perform better than tile sets without any error-control mechanism, and the performance improves as n increases. It is also proved that the error rates in assemblies formed by the 1-way and 2-way tile sets are O(epsilon^2), where epsilon is the error rate in assemblies without any error correction. In the second part of this thesis, we focus on a different error mechanism, namely,errors caused by imperfect or malformed tiles. We propose a model of malformed tiles, and consider the performance of various proofreading tile sets in the presence of malformed tiles. Our simulation results show that the Reif et al. 3-way overlay tile sets are able to best deal with malformed tiles. During the simulations, we observed that snaked proofreading tile sets always have trouble completing whole patterns when malformed tiles are present. We instead propose two modified snaked proofreading constructions, and verify through both simulations and analysis that the two modified constructions have much better performances. / Thesis (Master, Mathematics & Statistics) -- Queen's University, 2009-08-25 11:10:39.142

Les nanotechnologies ADN utilisées pour l’auto-assemblage de nanoparticules d’or ou de métaux nobles ont connu un important développement au cours des vingt dernières années, permettant l’organisation de particules agencées en nano-cristaux, grâce à la spécificité biologique inégalable de deux brins complémentaires d’ADN. L’objectif de ces travaux de thèse est d’adapter ces nanotechnologies à l’assemblage de nanoparticules d’Al et de CuO en vue d’élaborer des matériaux composites énergétiques à haute performance, grâce à l’augmentation des surfaces en contact entre réducteur (Al) et oxydant (CuO) par la maîtrise de l’organisation spatiale des nanoparticules. Ainsi, la fonctionnalisation séparée des nanoparticules d’Al et de CuO dispersées en solution colloïdale par des monobrins d’ADN complémentaires assurée ici par l’utilisation du complexe biotineStreptavidine, doit amener, après mélange des deux solutions colloïdales, à l’agrégation des particules par l’hybridation des brins d’ADN greffés en surface. La stratégie de fonctionnalisation choisie ici est générique : la protéine « Streptavidine » est d’abord greffée sur la nanoparticule, puis le brin d’ADN possédant un groupe biotine à une de ses extrémités, se fixe sur la Streptavidine. Au-delà de l’organisation de la matière à l’échelle nanométrique, l’enjeu double de ces travaux tient dans l’établissement d’un protocole de fonctionnalisation fiable et reproductible, propre aux procédés de micro-électronique, pour envisager un report de ces matériaux sur puce, mais également dans le contrôle des performances énergétiques grâce à l’ADN. Nous nous sommes donc appliqués à élaborer ce protocole en caractérisant précisément chaque étape de fonctionnalisation : la stabilisation des colloïdes et la biofonctionnalisation des nanoparticules par la Streptavidine et l’ADN. De plus, l’interaction entre ADN et surfaces oxydées des particules a été étudiée de façon à identifier les interactions non-spécifiques à l’origine d’agrégations non maîtrisées et améliorer en conséquence la qualité de la fonctionnalisation. Nous avons ensuite étudié l’agrégation des particules fonctionalisées en fonction de nombreux paramètres expérimentaux telles que la longueur de la chaîne ADN, la séquence de l’oligonucléotide, ou encore la composition saline de la solution. A cause de l’existence d’interactions non-spécifiques mise en évidence, nous avons optimisés ces paramètres de façon à assurer une agrégation dirigée uniquement par l’hybridation des brins d’ADN. Les performances énergétiques des matériaux synthétisés ont enfin été caractérisées et nous avons démontré la possibilité de contrôler les performances énergétiques des nanobiocomposites synthétisant en maîtrisant leur microstructure grâce à l’ADN. / Over the two last decades, DNA technologies have intensively been studied for the organization of matter at the nanoscale. Thanks to the bio recognition of two complementary DNA single-strands and their hybridization into the famous helicoidally structure, self-assembling of gold nanoparticles into highly ordered micrometer scale crystals has been demonstrated. The aim of this thesis is to explore this new nanotechnology for the self-assembly of Al and CuO nanoparticles driven by DNA hybridization into highly energetic nanocomposites by optimizing contact surfaces between reducer (Al) and oxidizer (CuO). We chose Streptavidin-biotin strategy to functionalize nanoparticles with DNA single strands. More precisely, the functionalization process includes four steps: (i) stabilization of Al and CuO nanoparticles into separate colloidal suspensions; (ii) Streptavidin grafting on Al and CuO nanoparticles; (iii) DNA grafting on Al and CuO Streptavidin-modified nanoparticles thanks to the addition of biotin function at the end of the DNA single strands; (iv) mixing of the two colloidal DNA-functionalized suspensions in order to realize the self-assembly. First, we precisely determined, characterized and optimized each step of the functionalization process. Then, we studied more precisely two key points of the process: we analyzed the interaction of DNA bases with technologically relevant oxide surfaces by studying the grafting of Thymidine by theoretical and experimental approaches; and we studied the influence of the coding sequence used for the DNA strands on the quality of the self-assembly, also by theoretical and experimental analyses. Finally, we optimized environmental conditions to realize the self-assembly of DNAfunctionalized nanoparticles into energetic nanobiocomposites. Morphologies and energetic properties were established as a function of synthesis conditions, and the control of energetic performances of nanobiocomposites as a function of aggregation process was demonstrated.

DNA nanotechnology is a rapidly developing field that creates nanoscale devices from DNA, which enables novel interfaces with biological material. Their therapeutic use is envisioned and applications in other areas of basic science have already been found. These devices function at physiological conditions and, owing to their molecular scale, are subject to thermal fluctuations during both preparation and operation of the device. Troubleshooting a failed device is often difficult and we develop models to characterise two separate devices: DNA walkers and DNA origami. Our framework is that of continuous-time Markov chains, abstracting away much of the underlying physics. The resulting models are coarse but enable analysis of system-level performance, such as ‘the molecular computation eventually returns the correct answer with high probability’. We examine the applicability of probabilistic model checking to provide guarantees on the behaviour of nanoscale devices, and to this end we develop novel model checking methodology. We model a DNA walker that autonomously navigates a series of junctions, and we derive design principles that increase the probability of correct computational output. We also develop a novel parameter synthesis method for continuous-time Markov chains, for which the synthesised models guarantee a predetermined level of performance. Finally, we develop a novel discrete stochastic assembly model of DNA origami from first principles. DNA origami is a widespread method for creating nanoscale structures from DNA. Our model qualitatively reproduces experimentally observed behaviour and using the model we are able to rationally steer the folding pathway of a novel polymorphic DNA origami tile, controlling the eventual shape.