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Dna origami

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https://www.readbyqxmd.com/read/28920942/exponential-growth-and-selection-in-self-replicating-materials-from-dna-origami-rafts
#1
Xiaojin He, Ruojie Sha, Rebecca Zhuo, Yongli Mi, Paul M Chaikin, Nadrian C Seeman
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating...
September 18, 2017: Nature Materials
https://www.readbyqxmd.com/read/28912216/a-cargo-sorting-dna-robot
#2
Anupama J Thubagere, Wei Li, Robert F Johnson, Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, Sarah Wittman, Niranjan Srinivas, Damien Woods, Erik Winfree, Lulu Qian
Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their destinations allows for a simple robot design: a single-stranded DNA with one leg and two foot domains for walking, and one arm and one hand domain for picking up and dropping off cargos. The robot explores a two-dimensional testing ground on the surface of DNA origami, picks up multiple cargos of two types that are initially at unordered locations, and delivers them to specified destinations until all molecules are sorted into two distinct piles...
September 15, 2017: Science
https://www.readbyqxmd.com/read/28902974/a-dna-origami-mechanical-device-for-the-regulation-of-microcosmic-structural-rigidity
#3
Neng Wan, Zhouping Hong, Huading Wang, Xin Fu, Ziyue Zhang, Chao Li, Han Xia, Yan Fang, Maoteng Li, Yi Zhan, Xiangliang Yang
DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states...
September 13, 2017: Small
https://www.readbyqxmd.com/read/28901745/terminating-dna-tile-assembly-with-nanostructured-caps
#4
Deepak K Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M Mohammed, Tyler D Jorgenson, Rebecca Schulman
Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes...
September 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28895291/revolving-vernier-mechanism-controls-size-of-linear-homomultimer
#5
Takeo Uchida, Keita Abe, Yuma Endo, Shosei Ichiseki, Satoru Akita, Shiyun Liu, Sho Aradachi, Masataka Saito, Akihiko Fukuchi, Taiyo Kikkawa, Theo Dammaretz, Ibuki Kawamata, Yuki Suzuki, Shin-Ichiro M Nomura, Satoshi Murata
A new kind of the Vernier mechanism that is able to control the size of linear assembly of DNA origami nanostructures is proposed. The mechanism is realized by mechanical design of DNA origami, which consists of a hollow cylinder and a rotatable shaft in it connected through the same scaffold. This nanostructure stacks with each other by the shape complementarity at its top and bottom surfaces of the cylinder, while the number of stacking is limited by twisting angle of the shaft. Experiments have shown that the size distribution of multimeric assembly of the origami depends on the twisting angle of the shaft; the average lengths of the multimer are decamer, hexamer, and tetramer for 0°, 10°, and 20° twist, respectively...
September 12, 2017: Small
https://www.readbyqxmd.com/read/28876958/directional-growth-of-dna-functionalized-nanorods-to-enable-continuous-site-specific-metallization-of-dna-origami-templates
#6
Bibek Uprety, John Jensen, Basu R Aryal, Robert C Davis, Adam T Woolley, John N Harb
This work examines anisotropic electroless plating of DNA-functionalized gold nanorods attached to a DNA origami template to fabricate continuous metal structures of rectangle, square and T shapes. DNA origami, a versatile method for assembling a variety of 2- and 3-D nanostructures, is utilized to construct the DNA breadboard template used for this study. Staple strands on selective sites of the breadboard template are extended with an additional nucleotide sequence for attachment of DNA-functionalized gold nanorods to the template via base pairing...
September 6, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28873273/docking-of-antibodies-into-cavities-in-dna-origami
#7
Xiangyuan Ouyang, Mattia De Stefano, Abhichart Krissanaprasit, Anne Louise Bank Kodal, Christian Bech Rosen, Tianqiang Liu, Sarah Helmig, Chunhai Fan, Kurt Vesterager Gothelf
Immobilized antibodies are extensively employed for medical diagnostics such as in enzyme-linked immunosorbent assays. Despite their widespread use the ability to control the orientation on surfaces of immobilized antibodies is very limited. Herein, we report a method for covalent and orientation-selective immobilization of antibodies in designed cavities in 2D and 3D DNA origami structures. Two tris(NTA) modified strands are inserted into the cavity to form NTA-metal complexes with histidine clusters on the Fc domain...
September 5, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28871786/fast-background-free-dna-paint-imaging-using-fret-based-probes
#8
Alexander Auer, Maximilian Thomas Strauss, Thomas Schlichthaerle, Ralf Jungmann
DNA points accumulation in nanoscale topography (DNA-PAINT) enables super-resolution microscopy by harnessing the predictable, transient hybridization between short dye-labeled 'imager' and complementary target-bound 'docking' strands. DNA-PAINT microscopy allows sub-5-nm spatial resolution, spectrally unlimited multiplexing and quantitative image analysis. However, these abilities come at the cost of non-fluorogenic imager strands, also emitting fluorescence when not bound to their docking strands. This has thus far prevented rapid image acquisition with DNA-PAINT, as the blinking rate of probes is limited by an upper-bound of imager strand concentrations, which in turn is dictated by the necessity to facilitate detection of single-molecule binding events over the background of unbound, freely diffusion probes...
September 5, 2017: Nano Letters
https://www.readbyqxmd.com/read/28869419/sub-10-nm-patterning-with-dna-nanostructures-a-short-perspective
#9
Ke Du, Myeongkee Park, Junjun Ding, Huan Hu, Zheng Zhang
DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ~10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either "top-down" or "bottom-up" approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. The perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography...
September 4, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28868629/afm-imaging-of-hybridization-chain-reaction-mediated-signal-transmission-between-two-dna-origami-structures
#10
Sarah Helmig, Kurt Vesterager Gothelf
Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-ranging signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins - of which one is immobilized in specific points along tracks on DNA origami structures - are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM)...
September 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28858402/fullerene-cluster-assisted-self-assembly-of-short-dna-strands-into-semiconducting-nanowires
#11
Sandeepa Kulala Vittala, Sajena Kanangat Saraswathi, Joshy Joseph
Programmable, hierarchical assembly of DNA nanostructures with the precise organization of functional components have been demonstrated previously with tiled assembly and DNA Origami. However, building organized nanostructures with random oligonucleotide strands remains as an elusive problem. Herein, we describe a simple and general strategy in which nanoclusters of a fullerene derivative act as stapler motifs in bringing ordered nanoscale assembly of short oligonucleotide duplexes into micrometer-sized nanowires...
August 31, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28842529/structure-of-the-holliday-junction-applications-beyond-recombination
#12
REVIEW
P Shing Ho
The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami...
August 24, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28833683/self-assembly-of-heterogeneously-shaped-nanoparticles-into-plasmonic-metamolecules-on-dna-origami
#13
Wenyan Liu, Ling Li, Shuo Yang, Jie Gao, Risheng Wang
Fabrication of plasmonic metamolecules (PMs) with rationally designed complexity is one of the major goals of nanotechnology. Most self-assembled PMs, however, have been constructed using single-component systems. The corresponding plasmonic assemblies still suffer from the lack of complexity, which is required to achieve a high degree of functionality. Here we report a general applicable strategy that can realize a series of high-ordered hetero-PMs using bottom-up DNA self-assembly. DNA functionalized differently-shaped nanoparticles were deliberately arranged in prescribed positions on 3D triangular DNA origami frames to form various hetero-PMs...
August 23, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28816436/integrated-distance-based-origami-paper-analytical-device-for-one-step-visualized-analysis
#14
Tian Tian, Yuan An, Yiping Wu, Yanling Song, Zhi Zhu, Chaoyong Yang
An integrated distance-based origami paper analytical device (ID-oPAD) is developed for simple, user friendly and visual detection of targets of interest. The platform enables complete integration of target recognition, signal amplification, and visual signal output based on aptamer/invertase-functionalized sepharose beads, cascaded enzymatic reactions, and a 3D microfluidic paper-based analytical device with distance-based readout, respectively. The invertase-DNA conjugate is released upon target addition, after which it permeates through the cellulose and flows down into the bottom detection zone, whereas sepharose beads with larger size are excluded and stay in the upper zone...
September 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28808731/biomacromolecules-as-tools-and-objects-in-nanometrology-current-challenges-and-perspectives
#15
Payam Hashemi, Luise Luckau, Petra Mischnick, Sarah Schmidt, Rainer Stosch, Bettina Wünsch
Nucleic acids, proteins, and polysaccharides are the most important classes of biopolymers. The inherent properties of biomacromolecules are contrary to those of well-defined small molecules consequently raising a number of specific challenges which become particularly apparent if biomacromolecules are treated as objects in quantitative analysis. At the same time, their specific functional ability of molecular recognition and self-organization (e.g., enzymes, antibodies, DNA) enables us to make biomacromolecules serving as molecular tools in biochemistry and molecular biology, or as precisely controllable dimensional platforms for nanometrological applications...
August 14, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28759871/dna-origami-nanorobot-fiber-optic-genosensor-to-tmv
#16
Emanuela Torelli, Marisa Manzano, Sachin K Srivastava, Robert S Marks
In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution...
July 21, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28750513/a-dna-walker-as-a-fluorescence-signal-amplifier
#17
Dongfang Wang, Carolin Vietz, Tim Schröder, Guillermo Acuna, Birka Lalkens, Philip Tinnefeld
Sensing nucleic acids typically involves the recognition of a specific sequence and reporting by, for example, a fluorogenic reaction yielding one activated dye molecule per detected nucleic acid. Here, we show that after binding to a DNA origami track a bound DNA target (a "DNA walker") can release the fluorescence of many molecules by acting as the catalyst of an enzymatic nicking reaction. As the walking kinetics sensitively depends on the walker sequence, the resulting brightness distribution of DNA origamis is a sequence fingerprint with single-nucleotide sensitivity...
September 13, 2017: Nano Letters
https://www.readbyqxmd.com/read/28745060/tunable-fluorescence-of-a-semiconducting-polythiophene-positioned-on-dna-origami
#18
Johanna Zessin, Franziska Fischer, Andreas Heerwig, Alfred Kick, Susanne Boye, Manfred Stamm, Anton Kiriy, Michael Mertig
A novel approach for the integration of π-conjugated polymers (CPs) into DNA-based nanostructures is presented. Using the controlled Kumada catalyst-transfer polycondensation, well-defined thiophene-based polymers with controllable molecular weight, specific end groups, and water-soluble oligoethylene glycol-based side chains were synthesized. The end groups were used for the easy but highly efficient click chemistry-based attachment of end-functionalized oligodeoxynucleotides (ODNs) with predesigned sequences...
July 27, 2017: Nano Letters
https://www.readbyqxmd.com/read/28738444/protein-coating-of-dna-nanostructures-for-enhanced-stability-and-immunocompatibility
#19
Henni Auvinen, Hongbo Zhang, Nonappa, Alisa Kopilow, Elina H Niemelä, Sami Nummelin, Alexandra Correia, Hélder A Santos, Veikko Linko, Mauri A Kostiainen
Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions...
July 24, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28737747/a-spatially-localized-architecture-for-fast-and-modular-dna-computing
#20
Gourab Chatterjee, Neil Dalchau, Richard A Muscat, Andrew Phillips, Georg Seelig
Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful design principle for overcoming limitations of speed and modularity in engineered molecular circuits. We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami. Signal propagation is demonstrated across transmission lines of different lengths and orientations and logic gates are modularly combined into circuits that establish the universality of our approach...
September 2017: Nature Nanotechnology
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