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Dna origami

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https://www.readbyqxmd.com/read/28714559/how-we-make-dna-origami
#1
Klaus F Wagenbauer, Floris A S Engelhardt, Evi K Stahl, Vera K Hechtl, Pierre Stömmer, Fabian Seebacher, Letizia Meregalli, Philip Ketterer, Thomas Gerling, Hendrik Dietz
DNA ORIGAMI has attracted substantial attention since its invention ten years ago due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. While the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality, and preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge...
July 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28710838/enzyme-free-ligation-of-5-phosphorylated-oligodeoxynucleotides-in-a-dna-nanostructure
#2
Markus Kramer, Clemens Richert
Multicomponent reactions are difficult synthetic transformations. For DNA, there is a special opportunity to align multiple strands in a folded nanostructure, so that they are preorganized to give a specific sequence. Multistrand reactions in DNA origami structures have previously been performed using photochemical crosslinking, 1,3-diploar cycloadditions or phosphoramidate-forming reactions. Here we report carbodiimide-driven phosphodiester formation in a small origami sheet that produces DNA strands up to 600 nucleotides in length in a single step...
July 15, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28702671/self-assembly-of-porphyrin-dna-hybrids-into-large-flat-nanostructures
#3
G Chatelain, G Clavé, C Saint-Pierre, D Gasparutto, S Campidelli
The main aim of nanotechnology is to create functional systems by controlling the matter at the nanometer level. In this context DNA is a versatile building block for the fabrication of micrometer-scale objects with a subnanometer-scale resolution. Over the last 15 years, DNA nanotechnology has considerably developed with the invention of DNA origami, double crossover structures and molecule/oligonucleotide hybrids. Our interest is focused on the combination of short complementary DNA sequences with organic molecules with a view to create large self-assembled nanostructures...
July 12, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28691083/sub-100-nm-metafluorophores-with-digitally-tunable-optical-properties-self-assembled-from-dna
#4
Johannes B Woehrstein, Maximilian T Strauss, Luvena L Ong, Bryan Wei, David Y Zhang, Ralf Jungmann, Peng Yin
Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28681899/allosteric-control-of-nanomechanical-dna-origami-pinching-devices-for-enhanced-target-binding
#5
Akinori Kuzuya, Yusuke Sakai, Takahiro Yamazaki, Yan Xu, Yusei Yamanaka, Yuichi Ohya, Makoto Komiyama
Significant enhancement of single-molecular binding to a miRNA target and bidentate and asymmetric conjugation of two distinct thiolated DNA strands to single gold nanoparticles (AuNPs) were visibly demonstrated, by introducing two groups of ligands into our nanomechanical DNA origami devices (DNA pliers) to construct allosterically controllable systems.
July 6, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28681897/solid-surface-vs-liquid-surface-nanoarchitectonics-molecular-machines-and-dna-origami
#6
Katsuhiko Ariga, Taizo Mori, Waka Nakanishi, Jonathan P Hill
The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment...
July 6, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28679055/origami-arrays-as-substrates-for-the-determination-of-reaction-kinetics-using-high-speed-atomic-force-microscopy
#7
Masudur Rahman, B Scott Day, David Neff, Michael L Norton
DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s...
July 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28670830/resonant-formation-of-strand-breaks-in-sensitized-oligonucleotides-induced-by-low-energy-electrons-0-5-9-0-ev
#8
Ilko Bald, Robin Schürmann, Thupten Tsering, Tanzer Katrin, Stephan Denifl, S V K Kumar
Halogenated nucleobases act as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) via dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over a broad range of electron energies in which DEA can take place (< 12 eV)...
July 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28654269/versatile-dna-origami-nanostructures-in-simplified-and-modular-designing-framework
#9
Yan Cui, Ruipeng Chen, Mingxuan Kai, Yaqi Wang, Yongli Mi, Bryan Wei
We introduce a simplified and modular architecture for design and construction of complex origami nanostructures. A series of basic two-dimensional and three-dimensional structures are presented. As the resulting structures can be virtually divided into blocks, modular remodeling such as translocation, contraction/extension, and bending is carried out. Structures under such a designing framework are morphable. Local conformational changes can propagate to the entire structure to reshape the global conformation...
July 6, 2017: ACS Nano
https://www.readbyqxmd.com/read/28651051/molecular-precision-at-micrometer-length-scales-hierarchical-assembly-of-dna-protein-nanostructures
#10
Daniel Schiffels, Veronika A Szalai, J Alexander Liddle
Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method...
July 3, 2017: ACS Nano
https://www.readbyqxmd.com/read/28650478/a-dna-origami-platform-for-quantifying-protein-copy-number-in-super-resolution
#11
Francesca Cella Zanacchi, Carlo Manzo, Angel S Alvarez, Nathan D Derr, Maria F Garcia-Parajo, Melike Lakadamyali
Single-molecule-based super-resolution microscopy offers researchers a unique opportunity to quantify protein copy number with nanoscale resolution. However, while fluorescent proteins have been characterized for quantitative imaging using calibration standards, similar calibration tools for immunofluorescence with small organic fluorophores are lacking. Here we show that DNA origami, in combination with GFP antibodies, is a versatile platform for calibrating fluorophore and antibody labeling efficiency to quantify protein copy number in cellular contexts using super-resolution microscopy...
June 26, 2017: Nature Methods
https://www.readbyqxmd.com/read/28639303/an-addressable-2d-heterogeneous-nanoreactor-to-study-the-enzyme-catalyzed-reaction-at-the-interface
#12
Dianming Wang, Guoliang Zhang, Yiyang Zhang, Ling Xin, Yuanchen Dong, Yang Liu, Dongsheng Liu
Membrane plays significant role in cellular enzymatic reactions. To better understand its function on membrane integral or bound enzymes, DNA origami and frame-guided assembly strategy are combined to construct a given-size, addressable enzyme-containing nanomembrane as a heterogeneous reactor to explore the enzymatic catalyst reaction on the membrane. The enzymes in the membrane are located precisely. This new kind of membrane can enrich hydrophobic substrate molecules in aqueous solution to the embedded enzymes...
June 22, 2017: Small
https://www.readbyqxmd.com/read/28629010/fabrication-of-dna-nanotubes-with-an-array-of-exterior-magnetic-nanoparticles
#13
Adele Rafati, Ali Zarrabi, Pooria Gill
Described here a methodology for arraying of magnetic nanoparticles (MNPs) on the surface of DNA nanotubes (DNTs). Positioning of magnetic nanoparticles at exterior surface of DNTs were shaped after self-assembling of oligonucleotide staples within an M13mp18 DNA scaffold via an origami process. The staples were partially labeled with biotin to be arrayed at the surface of DNTs. Gel retardation assay of the DNTs carrying magnetic nanoparticles indicated a reversely behavioral electrophoretic movement in comparison to the nanotubes have been demonstrated previously...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28620911/distortion-of-dna-origami-on-graphene-imaged-with-advanced-tem-techniques
#14
Yoones Kabiri, Adithya N Ananth, Jaco van der Torre, Allard Katan, Jin-Yong Hong, Sairam Malladi, Jing Kong, Henny Zandbergen, Cees Dekker
While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes...
June 16, 2017: Small
https://www.readbyqxmd.com/read/28618781/cavity-type-dna-origami-based-plasmonic-nanostructures-for-raman-enhancement
#15
Mengzhen Zhao, Xu Wang, Shaokang Ren, Yikang Xing, Jun Wang, Nan Teng, Dongxia Zhao, Wei Liu, Dan Zhu, Shao Su, Jiye Shi, Shiping Song, Lihua Wang, Jie Chao, Lianhui Wang
DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template...
June 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28616969/ph-driven-actuation-of-dna-origami-via-parallel-i-motif-sequences-in-solution-and-on-surfaces
#16
Jacob M Majikes, Lucas C C Ferraz, Thomas H LaBean
As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures...
June 27, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28609612/diverse-supramolecular-nanofiber-networks-assembled-by-functional-low-complexity-domains
#17
Bolin An, Xinyu Wang, Mengkui Cui, Xinrui Gui, Xiuhai Mao, Yan Liu, Ke Li, Cenfeng Chu, Jiahua Pu, Susu Ren, Yanyi Wang, Guisheng Zhong, Timothy K Lu, Cong Liu, Chao Zhong
Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multi-block and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities...
June 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/28605177/dna-origami-scaffolds-for-creating-higher-order-structures
#18
Fan Hong, Fei Zhang, Yan Liu, Hao Yan
DNA has become one of the most extensively used molecular building blocks for engineering self-assembling materials. DNA origami is a technique that uses hundreds of short DNA oligonucleotides, called staple strands, to fold a long single-stranded DNA, which is called a scaffold strand, into various designer nanoscale architectures. DNA origami has dramatically improved the complexity and scalability of DNA nanostructures. Due to its high degree of customization and spatial addressability, DNA origami provides a versatile platform with which to engineer nanoscale structures and devices that can sense, compute, and actuate...
June 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28598482/correction-structural-stability-of-dna-origami-nanostructures-in-the-presence-of-chaotropic-agents
#19
Saminathan Ramakrishnan, Georg Krainer, Guido Grundmeier, Michael Schlierf, Adrian Keller
Correction for 'Structural stability of DNA origami nanostructures in the presence of chaotropic agents' by Saminathan Ramakrishnan et al., Nanoscale, 2016, 8, 10398-10405.
June 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/28586869/unfolding-the-clinical-potential-of-dna-and-protein-origami
#20
Tracy Hampton
No abstract text is available yet for this article.
June 6, 2017: JAMA: the Journal of the American Medical Association
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