No description available.

DNA provides an ideal substrate for nanoscale construction and programmable dynamic mechanisms. DNA mechanisms can be used to produce DNA motors which do mechanical work, e.g. transportation of a substrate along a track. I explore a method for control of a DNA mechanism ubiquitous in DNA motor designs, toehold-mediated strand displacement, by which one strand in a duplex can be swapped for another. My method uses a mismatch between a pair of nucleotides in the duplex, which is repaired by displacement. I find that displacement rate can be fine-tuned by adjusting the position of the mismatch in the duplex, enabling the design of complex kinetic behaviours. A bipedal motor [1, 2] is designed to walk along a single-stranded DNA track. Previously the motor has only taken a single step, due to a lack of designs to extend the single-stranded track. I present a novel design for track held under tension using a 3D DNA origami tightrope, and verify its assembly. The bipedal motor design is adapted and a method to specifically place motors on tightropes is demonstrated. Motor operation is investigated on truncated tracks and tightrope tracks by electrophoresis and spectrofluorometry. The motor does not accumulate appreciably at the track end; this is tentatively attributed to rearrangement of the motor between track sites without interaction with fuel. Tightrope origami can hold single-stranded DNA under pN tension. I use tightropes to study hybridization kinetics under tension and find dramatic, non-monotonic changes in hybridization rate constants and dissociation constants with tension in the range ∼0-15 pN. Extended tracks for a 'burnt-bridges' motor which destroys its track as it moves [3] are created on the inside of DNA nanotubes, which can be polymerised to create tracks up to a few mm in length, and on tiles which I attempt to join in a specific order. Crossing of the motor between tubes is verified, and microscopy experiments provide some evidence that track is being cleaved by the motor, a requirement for movement along the track. Tile based tracks are imaged by super-resolution DNA PAINT [4], providing proof-of-principle for track observation to infer motor movement.

Much of our knowledge of cellular biology arises from direct observation of active cellular functions. Tools and techniques have steadily developed over the past several hundreds of years to aid in our understanding and control of the nanoworld and are referred to as nanotechnologies. In the context of nanotechnology, DNA is not used as a carrier for genetic information (as it is in cell), but as a construction material. DNA offers unprecedented control over the construction of simplified biomimetic models for the study of biological processes. This thesis first introduces and defines the field of DNA nanotechnology, with particular emphasis on the interaction of snthetic DNA nanostructures with biological membranes. Inspired by the protein clathrin, three-fold symmetric DNA tile made of eight, short DNA strands and capable of polymerising is described and studied, with the aim to interact with and controllably bend a membrane bilayer. This structure presented challenges during construction so an enhanced three-armed DNA structure built with DNA origami was designed. The succesful assembly of a rigid and functionalisable nanostructure is described. This origami structure was polymerised into large constructs in solution and on a supported lipid membrane. The shape of the structure was modulated to vary its curvature and apply a bending force to a lipid vesicle when anchored to it. Following the conclusion of this study, we present the construction of a small, unique DNA structure for enhanced electron microscopy imaging in cell lysate. This project is part of a developing technique to couple the interaction specificity of dyes in super-resolution microscopy and the high-resolution output of electron microscopy. Finally, the optimisation procedures and recommendations for TEM imaging of samples of DNA origami and lipid structures are discussed.

Plasmonic cavities confine optical fields at metal-dielectric interfaces via collective charge oscillations of free electrons within metals termed surface plasmon polaritons (SPPs). SPPs are confined in nanometre gaps formed between two metallic surfaces which creates an optical resonance. This optical resonance of the system is controlled by the geometry and the material of the nanogap. The focus of this work is to understand and utilize these confined optical modes to probe and manipulate the dynamics of single-molecules at room temperature. In this thesis, nanogap cavities are constructed by placing nanoparticles on top of a metal-film separated by molecular spacers. Such nanogaps act as cavities with confined optical fields in the gap. Precise position and orientation of single-molecules in the gap is obtained by supramolecular guest-host assembly and DNA origami breadboards. The interaction of light and single-molecules is studied in two different regimes of interaction strength. In the perturbative regime molecular light emission from electronic and vibrational states is strongly enhanced and therefore is used for the detection of single-molecules. In this regime the energy states remain unaltered, however profound effects emerge when the gap size is reduced to < 1 nm. New hybridized energy states which are half-light and half-matter are then formed. Dispersion of these energies is studied by tuning the cavity resonance across the molecular resonance, revealing the anti-crossing signature of a strongly coupled system. This dressing of molecules with light results in the modification of photochemistry and photophysics of single-molecules, opening up the exploration of complex natural processes such as photosynthesis and the possibility to manipulate chemical bonds.

Les méthodes de microscopie de super-résolution (SRM) telles que la microscopie PALM (photoactivated localization microscopy), STORM (stochastic optical reconstruction microscopy), BALM (binding-activated localization microscopy) et le DNA-PAINT, représentent un nouvel ensemble de techniques de microscopie optique qui permettent de surpasser la limite de diffraction ( > 200 nm dans le spectre visible). Ces méthodes sont basées sur la localisation de la fluorescence de molécules uniques, et peuvent atteindre des résolutions de l'ordre du nanomètres (~20 nm latéralement et 50 nm axialement). Les techniques SRM ont un large spectre d'applications dans les domaines de la biologie et de la biophysique, rendant possible l'accès à l'information tant dynamique que structurale de structures connues ou non, in vivo et in vitro. Beaucoup d'efforts ont été fournis durant la dernière décennie afin d'élargir le potentiel de ces méthodes en développant des méthodes de localisation à la fois plus précise et plus rapide, d'améliorer la photophysique des fluorophores, de développer des algorithmes pour obtenir une information quantitative et augmenter la précision de localisation, etc. Cependant, très peu de méthodes ont été développées pour examiner l'hétérogénéité des images et extraire les informations statistiquement pertinent à partir de plusieurs milliers d'images individuelles super-résolues. Dans mon travail de thèse, je me suis spécifiquement attaquée à ces limitations en: (1) construisant des objets de dimensions nanométriques et de structures bien définies, avec la possibilité d'être adaptés aux besoins. Ces objets sont basés sur les origamis d'ADN. (2) développant des approches de marquage afin d'acquérir des images homogènes de ces objets. (3) implémentant des outils statistiques dans le but d'améliorer l'analyse et la validation d'images. Ces outils se basent sur des méthodes de reconstruction de molécules uniques communément appliquées aux reconstructions d'images de microscopie électronique. J'ai spécifiquement appliqué ces développements à la reconstruction de formes 3D de deux origamis d'ADN modèles (en une et trois dimensions). Je montre comment ces méthodes permettent la dissection de l'hétérogénéité de l'échantillon, et la combinaison d'images similaires afin d'améliorer le rapport signal sur bruit. La combinaison de différentes classes moyennes ont permis la reconstruction des formes tridimensionnelles des origamis d'ADN. Particulièrement, car cette méthode utilise la projection 2D de différentes vues d'une même structure, elle permet la récupération de résolutions isotropes en trois dimensions. Des fonctions spécifiques ont été adaptées à partir de méthodologies existantes afin de quantifier la fiabilité des reconstructions et de leur résolution. A l'avenir, ces développements seront utiles pour la reconstruction 3D de tous types d'objets biologiques pouvant être observés à haute résolution par des méthodologies dérivées de PALM, STORM ou PAINT. / Super resolution microscopy (SRM) methods such as photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), binding-activated localization microscopy (BALM) and DNA-PAINT represent a new collection of light microscopy techniques that allow to overpass the diffraction limit barrier ( > 200 nm in the visible spectrum). These methods are based on the localization of bursts of fluorescence from single fluorophores, and can reach nanometer resolutions (~20 nm in lateral and 50 nm in axial direction, respectively). SRM techniques have a broad spectrum of applications in the field of biology and biophysics, allowing access to structural and dynamical information of known and unknown biological structures in vivo and in vitro. Many efforts have been made over the last decade to increase the potential of these methods by developing more precise and faster localization techniques, to improve fluorophore photophysics, to develop algorithms to obtain quantitative information and increase localization precision, etc. However, very few methods have been developed to dissect image heterogeneity and to extract statistically relevant information from thousands of individual super-resolved images. In my thesis, I specifically tackled these limitations by: (1) constructing objects with nanometer dimensions and well-defined structures with the possibility of be tailored to any need. These objects are based on DNA origami. (2) developing labeling approaches to homogeneously image these objects. These approaches are based on adaptations of BALM and DNA-PAINT microscopies. (3) implemented statistical tools to improve image analysis and validation. These tools are based on single-particle reconstruction methods commonly applied to image reconstruction in electron microscopy.I specifically applied these developments to reconstruct the 3D shape of two model DNA origami (in one and three dimensions). I show how this method permits the dissection of sample heterogeneity, and the combination of similar images in order to improve the signal-to-noise ratio. The combination of different average classes permitted the reconstruction of the three dimensional shape of DNA origami. Notably, because this method uses the 2D projections of different views of the same structure, it permits the recovery of isotropic resolutions in three dimensions. Specific functions were adapted from previous methodologies to quantify the reliability of the reconstructions and their resolution.In future, these developments will be helpful for the 3D reconstruction of any biological object that can be imaged at super resolution by PALM, STORM or PAINT-derived methodologies.

No description available.

This work examines the selective deposition of metallic and semiconductor materials onto DNA templates for the fabrication of nanodevices. DNA origami provides a simple and robust method for folding DNA into a variety of shapes and patterns and makes it possible to create the complex templates needed for nanodevices, such as nanoelectronic circuits, plasmonics, and nanosensors. Metallization of DNA origami templates is essential for the fabrication of such nanodevices. In addition, selective deposition of semiconductor materials onto the DNA template is of importance for making many nanodevices such as nanocircuits. Metallization of DNA origami presents several challenges beyond those associated with the metallization of other DNA templates such as λ-DNA. All of these challenges were addressed in this study. DNA origami templates were seeded with Ag and then plated with Au via electroless deposition. Selective continuous metal deposition was achieved, with an average metallized height as small as 32 nm. The structure of T-shaped DNA origami was also retained after metallization. Following the metallization of complete origami, site-specific metallization of branched DNA origami was also demonstrated. To achieve this, staple strands at select locations on origami were replaced with staple strands modified with binding sites at the end. These binding sites then attached to thiolated DNA coated Au nanoparticles through base pairing. The continuous Au nanowires formed at designated sites on DNA origami after Au plating had an average width of 33 nm, with the smallest ones ~20 nm wide. The continuity of nanowires was verified by conductivity tests- the only tests of this nature of which I am aware. Moreover, predesigned sites on "circuit-shaped" DNA origami were successfully metallized. The selective deposition of a variety of materials onto DNA templates for the formation of continuous DNA-templated nanowires was also demonstrated. Specifically, an electroless Ni plating solution was developed to enable the fabrication of uniform and continuous DNA-templated Ni nanowires. Tests showed that these DNA-templated Ni nanowires were conductive. Moreover, continuous DNA-templated Bi2Te3 and/or Te nanowires have been fabricated through galvanic displacement of DNA-templated Ni and Cu nanowires. Altogether, these results represent important progress toward the realization of DNA-templated nanofabrication.

No description available.

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.

No description available.