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Dissertations / Theses on the topic 'DNA origami'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Dunn, Katherine Elizabeth. "DNA origami assembly." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:dff1bafd-e355-4df5-968b-b0deb7e6f44f.

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This thesis describes my investigations into the principles underlying self-assembly of DNA origami nanostructures and discusses how these principles may be applied. To study the origami folding process I designed, synthesized and characterized a polymorphic tile, which could adopt various shapes. The distribution of tile shapes provided new insights into assembly. The origami tiles I studied were based on scaffolds derived from customized plasmids, which I prepared using recombinant DNA technology. I developed a technique to monitor incorporation of individual staples in real time using fluor

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2

Seibert, Mark Marvin. "Protein Folding and DNA Origami." Doctoral thesis, Uppsala universitet, Molekylär biofysik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121549.

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In this thesis, the folding process of the de novo designed polypeptide chignolin was elucidated through atomic-scale Molecular Dynamics (MD) computer simulations. In a series of long timescale and replica exchange MD simulations, chignolin’s folding and unfolding was observed numerous times and the native state was identified from the computed Gibbs free-energy landscape. The rate of the self-assembly process was predicted from the replica exchange data through a novel algorithm and the structural fluctuations of an enzyme, lysozyme, were analyzed. DNA’s structural flexibility was investigate

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3

Marras, Alexander Edison. "DNA Origami Mechanisms and Machines." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366227349.

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4

Hazard, Octave. "Controlling DNA Origami Co-folding." Electronic Thesis or Diss., Lyon, École normale supérieure, 2025. http://www.theses.fr/2025ENSL0007.

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L’origami ADN est une technique particulièrement robuste permettant de concevoir des structures en ADN, souvent de l’ordre de la centaine de nanomètres. Introduite en 2006 par Paul Rothemund, cette technique repose sur le repliement contrôlé d’un long brin d’ADN appelé scaffold (de quelques milliers de nucléotides), au moyen d’un ensemble de brins synthétiques plus courts bien choisis, appelés agrafes. Elle se prête particulièrement bien à la conception de structures complexes en deux ou trois dimensions. Cependant, la taille de ces origamis ADN est limitée par la longueur du scaffold. Plusieu

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5

Daljit, Singh Jasleen Kaur. "Lipid-interacting switchable DNA origami nanostructures." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/28197.

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DNA nanotechnology allows for the programmable self-assembly of nanostructures of arbitrary shapes and sizes. DNA nanostructures can be hydrophobically modified for integration with lipid bilayers. Lipid-integrated DNA nanotechnology can allow for the study of membrane proteins and other fundamental biological processes. In this thesis, switchable lipid-interacting DNA origami nanostructures are introduced. First, dimeric DNA origami nanostructures are successfully programmed to monomerise upon switching. The design space of switchable DNA origami nanostructures is explored using molecular

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6

Boemo, Michael Austin. "Computation by origami-templated DNA walkers." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:bdea667e-a9aa-484a-9db0-a816339e5594.

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Interactions between DNA molecules can be used to perform computation. These DNA computing systems often use DNA molecules as freely diusing reactants in a well-mixed solution. We demonstrate how DNA walkers tethered to an origami-templated track can perform computation. A DNA walker can block a track that intersects with its own, preventing another walker from stepping down this blocked track. These blockages are primitive operations that can be used to perform computation. This thesis demonstrates how blocking interactions between DNA walkers can evaluate formulae posed in propositional logi

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7

Hudoba, Michael W. "Force Sensing Applications of DNA Origami Nanodevices." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1471474143.

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8

Darcy, Michael Augusto. "High Force Applications of DNA Origami Devices." The Ohio State University, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1619092851712077.

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9

Geng, Yanli. "Metallization of DNA and DNA Origami Using a Pd Seeding Method." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3857.

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In this dissertation, I developed a Pd seeding method in association with electroless plating, to successfully metallize both lambda DNA and DNA origami templates on different surfaces. On mica surfaces, this method offered a fast, simple process, and the ability to obtain a relatively high yield of metallized DNA nanostructures. When using lambda DNA as the templates, I studied the effect of Pd(II) activation time on the seed height and density, and an optimal activation time between 10 and 30 min was obtained. Based on the Pd seeds formed on DNA, as well as a Pd electroless plating solution,

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10

Marcus, Pierre. "Toward Scalable DNA algorithms." Electronic Thesis or Diss., Lyon, École normale supérieure, 2024. http://www.theses.fr/2024ENSL0024.

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Le domaine du calcul par ADN consiste à utiliser l'ADN comme un matériau dynamique. En interagissant ensemble, les brins d’ADN peuvent implémenter de petits algorithmes et effectivement calculer. Par exemple, l’état de l’art permet l’évaluation de circuits logiques, où les informations de l’évaluation des circuits sont encodées dans les reconfigurations d’assemblage de brins d'ADN. Un autre exemple d’approche consiste à attacher des brins d'ADN selon des règles définies, proches du Le domaine du calcul par ADN consiste à utiliser l'ADN comme un matériau dynamique. En interagissant ensemble, le

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11

Said, Hassan [Verfasser]. "Studien zu synthetischen DNA Origami-Strukturen / Hassan Said." München : Verlag Dr. Hut, 2016. http://d-nb.info/1094117692/34.

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12

Briggs, Emily N. "Scaffolded DNA Origami Nanotechnology for Receptor Ligand Studies." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1374169534.

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13

Marras, Alexander Edison. "Design, Control, and Implementation of DNA Origami Mechanisms." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1500576490237821.

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14

Ratanalert, Sakul. "Sequence design principles for 3D wireframe DNA origami." Thesis, Massachusetts Institute of Technology, 2018. https://hdl.handle.net/1721.1/121818.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2018<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 143-151).<br>DNA is a highly programmable molecule that can be designed to self-assemble into nearly arbitrary 2D and 3D nanoscale structures. DNA origami is a particularly versatile method to achieve complex molecular architectures. However, the rules for designing scaffolded DNA origami have not been well-formalized, which hinders both the investigation of characteristics of well- and poorly-folded structures as

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15

McDowell, Matthew Paul. "DNA Origami Stabilized and Seeded with 4'-Aminomethyltrioxsalen for Improved DNA Nanowire Fabrication." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/6001.

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A fast emerging technology in the microelectronics field is bottom-up self-assembly of computer circuitry. A promising method to develop nanoelectronic devices through bottom-up self-assembly is the implementation of DNA-based technologies. Using DNA to create nanoelectronic devices is advantageous because of its already well understood base-paring and annealing qualities. These base-pairing and annealing qualities can be used to design and construct DNA nanostructures called DNA origami. DNA origami are specially designed structures made from single stranded DNA. Short single stranded DNA oli

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16

Wang, Jing. "DNA-Origami Templated Formation of Liposomes and Related Structures." Thesis, Yale University, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3582201.

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<p> We have developed novel techniques for manufacturing vesicles with predefined attachments to scaffolds of DNA, and have studied the underlying mechanism(s) of this DNA directed vesicle formation by capturing intermediates. These DNA scaffolds are self-assembled by the origami method, which can use DNA as a programmable building block to form diverse structures: two-dimensional crystals, nanotubes, and three-dimensional wireframe nanopolyhedra [1-5]. </p><p> Nano-templated vesicles are prepared using rigid rings of bundled DNA. Single phosphatidyl ethanolamine (PE) lipids are coupled to t

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17

Bell, Nicholas Andrew William. "DNA origami nanopores and single molecule transport through nanocapillaries." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648810.

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18

Turowski, Daniel J. "Assembly and characterization of mesoscale DNA material systems based on periodic DNA origami arrays." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1374169645.

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19

Wickham, Shelley. "DNA origami : a substrate for the study of molecular motors." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.561126.

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DNA origami is a method for constructing 2-dimensional nanostructures with arbitrary shapes, by folding a long piece of viral genomic DNA into an extended pattern (Rothemund, 2006). In this thesis DNA origami nanostructures that in- corporate active transport are developed, by combining rectangular DNA origami tiles with either synthetic DNA motors, or the protein motor F1-ATPase. The transport of an autonomous, unidirectional, and processive 'burnt-bridges' DNA motor across an extended linear track anchored to a DNA origami tile is demonstrated. Ensemble fluorescence measurements are used to

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20

Stein, Ingo. "DNA origami as a tool for single-molecule fluorescence studies." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-144789.

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21

Nickels, Philipp [Verfasser], and Tim [Akademischer Betreuer] Liedl. "Force spectroscopy with DNA origami / Philipp Nickels ; Betreuer: Tim Liedl." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2017. http://d-nb.info/1132510945/34.

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22

Kramer, Markus [Verfasser]. "Studien zur kovalenten Vernetzung von DNA-Origami-Strukturen / Markus Kramer." München : Verlag Dr. Hut, 2018. http://d-nb.info/1155056760/34.

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23

Teshome, Bezuayehu, Stefan Facsko, and Adrian Keller. "Topography-controlled alignment of DNA origami nanotubes on nanopatterned surfaces." Royal Society of Chemistry, 2014. https://tud.qucosa.de/id/qucosa%3A36286.

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The controlled positioning of DNA nanostructures on technologically relevant surfaces represents a major goal along the route toward the full-scale integration of DNA-based materials into nanoelectronic and sensor devices. Previous attempts to arrange DNA nanostructures into defined arrays mostly relied on top-down lithographic patterning techniques combined with chemical surface functionalization. Here we combine two bottom-up techniques for nanostructure fabrication, i.e., self-organized nanopattern formation and DNA origami self-assembly, in order to demonstrate the electrostatic self-align

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24

Westover, Tyler Richard. "Electrical Characterization and Annealing of DNA Origami Templated Gold Nanowires." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8396.

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DNA origami templates have been studied due the versatility of shapes that can be designed and their compatibility with various materials. This has potential for future electronic applications. This work presents studies performed on the electrical properties of DNA origami templated gold nanowires. Using a DNA origami tile, gold nanowires are site specifically attached in a “C” shape, and with the use of electron beam induced deposition of metal, electrically characterized. These wires are electrically conductive with resistivities as low as 4.24 x 10-5 Ω-m. During moderate temperature proces

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25

Miller, Carl A. "Control of Dynamic DNA Origami Mechanisms Using Integrated Functional Components." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429812012.

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26

NGO, ANH TIEN. "Construction of An Artificial Metabolic Channeling System on DNA Origami." Kyoto University, 2015. http://hdl.handle.net/2433/199413.

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27

Tokura, Yu [Verfasser]. "Design of polymer nanoarchitectures by DNA origami technology / Yu Tokura." Ulm : Universität Ulm, 2018. http://d-nb.info/1154856380/34.

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28

Kielar, Charlotte [Verfasser]. "DNA origami nanostructures in biomedicine: Beyond drug delivery / Charlotte Kielar." Paderborn : Universitätsbibliothek, 2020. http://d-nb.info/1215177186/34.

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29

Yamamoto, Seigi. "Design and Evaluation of DNA Nano-devices Using DNA Origami Method and Fluorescent Nucleobase Analogues." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215338.

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30

Mollica, Molly Y. "DNA Origami Breadboard: A Platform for Cell Activation and Cell Membrane Functionalization." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1461163132.

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31

Zhou, Lifeng. "Design Modeling and Analysis of Compliant and Rigid-Body DNA Origami Mechanisms." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492793740662906.

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32

Johnson, Joshua A. Dr. "Control of DNA Origami from Self-Assembly to Higher-Order Assembly." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1577996668813983.

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33

Schüller, Verena. "DNA origami structures for applications in single molecule spectroscopy and nanomedicine." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-157179.

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34

Roller, Eva-Maria [Verfasser], and Tim [Akademischer Betreuer] Liedl. "DNA origami templated plasmonic nanostructures / Eva-Maria Roller ; Betreuer: Tim Liedl." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2016. http://d-nb.info/1176971840/34.

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35

Hemmig, Elisa Alina. "DNA origami structures for artificial light-harvesting and optical voltage sensing." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274005.

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In the past decade, DNA origami self-assembly has been widely applied for creating customised nanostructures with base-pair precision. In this technique, the unique chemical addressability of DNA can be harnessed to create programmable architectures, using components ranging from dye or protein molecules to metallic nanoparticles. In this thesis, we apply DNA nanotechnology for developing novel light-harvesting and optical voltage sensing nano-devices. We use the programmable positioning of dye molecules on a DNA origami plate as a mimic of a light-harvesting antenna complex required for photo

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36

Kucinic, Anjelica. "Reconfiguration, actuation, and higher order complexity of dynamic DNA origami assemblies." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587726893405925.

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37

Aryal, Basu Ram. "Bottom-Up Fabrication and Characterization of DNA Origami-Templated Electronic Nanomaterials." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/9041.

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This work presents the bottom-up fabrication of DNA origami-assembled metal nanowires and metal-semiconductor junctions, and their electrical characterization. Integration of metal and semiconductor nanomaterials into prescribed sites on self-assembled DNA origami has facilitated the fabrication of electronic nanomaterials, whereas use of conventional tools in their characterization combines bottom-up and top-down technologies. To expand the contemporary DNA-based nanofabrication into nanoelectronics, I performed site-specific metallization of DNA origami to create arbitrarily arranged gold na

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38

Gates, Elisabeth Pound. "Self-Assembled DNA Origami Templates for the Fabrication of Electronic Nanostructures." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/4000.

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An important goal of nanoscience is the self-assembly of nanoscale building blocks into complex nanostructures. DNA is an important and versatile building block for nanostructures because of its small size, predictable base pairing, and numerous sequence possibilities. I use DNA origami to design and fold DNA into predesigned shapes, to assemble thin, branched DNA nanostructures as templates for nanoscale metal features. Using a PCR-based scaffold strand generation procedure, several wire-like nanostructures with varying scaffold lengths were assembled. In addition, more complex prototype circ

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39

MASCIOTTI, VALENTINA. "Design of an environment-indipendent, tunable 3D DNA-origami plasmonic sensor." Doctoral thesis, Università degli Studi di Trieste, 2018. http://hdl.handle.net/11368/2919796.

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DNA origami nanotechnology engineers DNA as the building blocks of newly conceived self-assembled materials and devices. Due to its high degree of customization and its precise spatial addressability, DNA origami provides an unmatched platform for nanoscale structures and devices design. Gold nanoparticles (AuNP) have been largely investigated because of their peculiar optical properties and in particular their localized surface plasmon resonance (LSPR) that modifies significantly the electromagnetic environment in a thin shell around them, and provides a tool with unrivalled potential to tun

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40

Derr, Nathan Dickson. "Coordination of Individual and Ensemble Cytoskeletal Motors Studied Using Tools from DNA Nanotechnology." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10889.

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The cytoskeletal molecular motors kinesin-1 and cytoplasmic dynein drive many diverse functions within eukaryotic cells. They are responsible for numerous spatially and temporally dependent intracellular processes crucial for cellular activity, including cytokinesis, maintenance of sub-cellular organization and the transport of myriad cargos along microtubule tracks. Cytoplasmic dynein and kinesin-1 are processive, but opposite polarity, homodimeric motors; they each can take hundreds of thousands of consecutive steps, but do so in opposite directions along their microtubule tracks. These step

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41

Ma, Zhipeng. "Characterization of Self-Assembly Dynamics and Mechanical Properties of DNA Origami Nanostructures." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/217167.

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42

Luu, Minh Tri. "DNA barrel nanostructure - a programmable building block for hierarchical self-assembly." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/26725.

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DNA nanostructures with complex structures and functions are emerging as promising tools for realising new applications, such as nanorobotics and advanced materials. To date, the complexity achieved is still limited, due to shortcomings associated with current self-assembly methods. This thesis presents a new assembly scheme to build more complex nanostructures. DNA barrel nanostructures were used as 3D voxels to build up superstructures. A literature nanostructure design was adopted and improved for use in the proposed hierarchical assembly strategy. Modified barrel nanostructures (referred

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43

Goodman, Brian Kruzick. "Investigating Cytoskeletal Motor Mechanisms using DNA Nanotechnology." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11222.

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The microtubule cytoskeleton plays a vital role in the spatial-temporal organization of subcellular cargo required to maintain homeostasis and direct cell division. Cytoplasmic dynein and kinesin are opposite-polarity, microtubule-based motors that transport a wide variety of cargo throughout eukaryotic cells. While much is known about the stepping mechanism of kinesin from decades of study, cytoplasmic dynein's size and complexity has limited our understanding of its underlying motor mechanism. Here, a minimal, artificially-dimerized dynein motor was observed with two-color, near-simultane

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44

Uprety, Bibek. "Site-Specific Metallization of Multiple Metals on a Single DNA Origami Template." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/8808.

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This work examines the selective deposition of two different metals on the same DNA origami template for nanofabrication. DNA, with adjustable size and shape serves as a suitable template for fabricating metal junctions in the nanometer domain via bottom-up assembly. Bottom-up assembly utilizes the recognition capability of molecules like DNA to self-assemble and form structures. In this regard, DNA origami provides a useful means for forming nanostructures by folding single-stranded DNA into different two and three dimensional shapes. Selective deposition of metal on specific locations of a D

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45

Eickert, Gunter Erick. "Using Modular Preformed DNA Origami Building Blocks to Fold Dynamic 3D Structures." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397742084.

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46

Lucas, Alexandra. "Dynamic DNA motors and structures." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:5f0b0773-a7af-4edb-a6a2-790a0086553d.

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DNA nanotechnology uses the Watson-Crick base-pairing of DNA to self-assemble structures at the nanoscale. DNA nanomachines are active structures that take energy from the system to drive a programmed motion. In this thesis, a new design for a reversible DNA motor and an automatically regenerating track is presented. Ensemble fluorescence measurements observe motors walking along the same 42nm track three times. A second new motor was designed to allow motors on intersecting tracks to block each other, which can be used to perform logical computation. Multiple design approaches are discussed.

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47

Sandén, Camilla. "Nanostructures on a Vector : Enzymatic Oligo Production for DNA Nanotechnology." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-85985.

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The technique of DNA origami utilizes the specific and limited bonding properties of DNA to fold single stranded DNA sequences of various lengths to form a predesigned structure. One longer sequence is used as a scaffold and numerous shorter sequences called staples, which are all complementary to the scaffold sequence, are used to fold the scaffold into intricate shapes. The most commonly used scaffold is derived by extracting the genome of the M13 phage and the staples are usually chemically synthesized oligonucleotides. Longer single stranded sequences are difficult to synthesize with high

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48

Yang, Yangyang. "Artificially controllable nanodevices constructed by DNA origami technology: photofunctionalization and single molecule analysis." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188512.

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49

Wünsch, Bettina Verfasser], and Philip [Akademischer Betreuer] [Tinnefeld. "Fluoreszenz- und streuungsbasierte Einzelmolekülmikroskopie an DNA-Origami-Nanostrukturen / Bettina Wünsch ; Betreuer: Philip Tinnefeld." Braunschweig : Technische Universität Braunschweig, 2018. http://d-nb.info/1175816108/34.

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50

Khmelinskaia, Alena [Verfasser], and Petra [Akademischer Betreuer] Schwille. "DNA origami scaffolds to control lipid membrane shape / Alena Khmelinskaia ; Betreuer: Petra Schwille." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1170582761/34.

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