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DNA nanotechnology

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https://www.readbyqxmd.com/read/28817122/single-cell-mechanogenetics-using-monovalent-magnetoplasmonic-nanoparticles
#1
Ji-Wook Kim, Daeha Seo, Jung-Uk Lee, Kaden M Southard, Yongjun Lim, Daehyun Kim, Zev J Gartner, Young-Wook Jun, Jinwoo Cheon
Spatiotemporal interrogation of signal transduction at the single-cell level is necessary to answer a host of important biological questions. This protocol describes a nanotechnology-based single-cell and single-molecule perturbation tool, termed mechanogenetics, that enables precise spatial and mechanical control over genetically encoded cell-surface receptors in live cells. The key components of this tool are a magnetoplasmonic nanoparticle (MPN) actuator that delivers defined spatial and mechanical cues to receptors through target-specific one-to-one engagement and a micromagnetic tweezers (μMT) that remotely controls the magnitude of force exerted on a single MPN...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28816314/pt-supraparticles-with-controllable-dna-valences-for-programmed-nanoassembly
#2
Gaoli Chen, Song Wang, Lei Song, Xiaojun Song, Zhaoxiang Deng
Supraparticles are self-limiting nanoparticle ensembles with attractive properties from their unique hierarchical (primary and secondary) structures. Aiming at relieving the bottleneck of the very limited material building blocks in DNA nanotechnology, we herein demonstrate Pt-based supraparticles as catalytic materials for valence-controllable and high density DNA functionalizations toward DNA-programmed nanoassembly.
August 17, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28809101/a-microsphere-supported-lipid-bilayer-platform-for-dna-reactions-on-a-fluid-surface
#3
Aurora Fabry-Wood, Madalyn Elise Fetrow, Carl W Brown Iii, Nicholas A Baker, Nadiezda Fernandez Oropeza, Andrew P Shreve, Gabriel A Montano, Darko Stefanovic, Matthew R Lakin, Steven W Graves
We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (µSLBs) with membrane-bound nucleic acid components...
August 15, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28806061/construction-of-a-polyhedral-dna-12-arm-junction-for-self-assembly-of-wireframe-dna-lattices
#4
Ilenia Manuguerra, Guido Grossi, Rasmus P Thomsen, Jeppe Lyngsø, Jan Skov Pedersen, Jørgen Kjems, Ebbe Sloth Andersen, Kurt Vesterager Gothelf
A variety of different tiles for the construction of DNA lattices have been developed since the structural DNA nanotechnology field was born. The majority of these are designed for the realization of close-packed structures where DNA helices are arranged in parallel and tiles are connected through sticky ends. Assembly of such structures requires to the use of cation rich buffers to minimize repulsion between parallel helices, which poses limits to the application of DNA nanostructures. Wireframe structures on the other hand are less susceptible to salt concentration, but the assembly of wireframe lattices is limited by the availability of tiles and 2 motifs...
August 14, 2017: ACS Nano
https://www.readbyqxmd.com/read/28805877/a-dna-bipedal-nanowalker-with-a-piston-like-expulsion-stroke
#5
Q Y Yeo, I Y Loh, S R Tee, Y H Chiang, J Cheng, M H Liu, Z S Wang
Artificial molecular walkers beyond burn-bridge designs are important for nanotechnology, but their systematic development remains difficult. Herein, we have reported a new rationally designed DNA walker-track system and experimentally verified a previously proposed general expulsion regime for implementing non-burn-bridge nanowalkers. The DNA walker has an optically powered engine motif that reversibly extends and contracts the walker via a quadruplex-duplex conformational change. The walker's extension is an energy-absorbing and force-generating process, which drives the walker's leg dissociation off-track in a piston-like expulsion stroke...
August 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/28799656/review-of-the-effects-of-manufactured-nanoparticles-on-mammalian-target-organs
#6
REVIEW
Tianshu Wu, Meng Tang
Nanotechnology had matured significantly during the last two decades as it has transitioned from bench top science to applied technology. Even though the issue of safety of nanotechnology has been raised nearly one decade ago, the rapid progress in development and use of nanomaterials has not yet been matched by toxicological investigations. Many recent studies have simply outlined the toxic effects of nanoparticles (NPs), but few have systematically addressed their potentially adverse biological effects on target organs...
August 11, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28796345/photochemical-acceleration-of-dna-strand-displacement-using-ultrafast-dna-photo-cross-linking
#7
Shigetaka Nakamura, Hirokazu Hashimoto, Satoshi Kobayashi, Kenzo Fujimoto
DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In our body, DNA strand displacement is regulated and accelerated by enzymes. Furthermore, acceleration of DNA strand displacement is required for a rapid response of biological processes. In this study, we evaluated the DNA strand displacement using DNA photo-cross-linking to accelerate this displacement. The DNA photo-cross-linking of CNVK was accelerated at least 20 times, showing a faster DNA strand displacement...
August 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28794955/self-assembly-of-g-rich-oligonucleotides-incorporating-a-3-3-inversion-of-polarity-site-a-new-route-towards-g-wire-dna-nanostructures
#8
Giorgia Oliviero, Stefano D'Errico, Brunella Pinto, Fabrizia Nici, Principia Dardano, Ilaria Rea, Luca De Stefano, Luciano Mayol, Gennaro Piccialli, Nicola Borbone
Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions...
August 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28792224/supramolecular-protein-assemblies-based-on-dna-templates
#9
Chunxi Hou, Shuwen Guan, Ruidi Wang, Wei Zhang, Fanchao Meng, Linlu Zhao, Jiayun Xu, Junqiu Liu
DNA plays an important role in the process of protein assembly. DNA viruses such as M13 virus are typical examples in which single DNA genome behaves as template to induce multiple major coat protein (PⅧ) monomers assembling. Thus, design of protein assemblies based on DNA templatesattracts much interest in construction of supramolecular structructures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions and protein-adapter interactions...
August 9, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28791555/oxidative-damage-to-pseudomonas-aeruginosa-atcc-27833-and-staphylococcus-aureus-atcc-24213-induced-by-cuo-nps
#10
Ana Laura Ulloa-Ogaz, Hilda Amelia Piñón-Castillo, Laila Nayzzel Muñoz-Castellanos, Martha Samira Athie-García, María De Lourdes Ballinas-Casarrubias, José Guadalupe Murillo-Ramirez, Luis Ángel Flores-Ongay, Robert Duran, Erasmo Orrantia-Borunda
The cytotoxicity of nanoparticles (NPs) and their properties are important issues in nanotechnology research. Particularly, NPs affect the metabolism of microorganisms due to NP interactions with some biomolecules. In order to assess the mechanisms underlying NPs toxicity, we studied the damage caused by copper oxide nanoparticles (CuO-NPs) on Staphylococcus aureus ATCC 24213 and Pseudomonas aeruginosa ATCC 27833. Spherical CuO-NPs characterized by their diameter (13 ± 3 nm) were synthesized with a maximum of 254 nm...
August 8, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28771915/dna-arrays-with-a-silver-lining
#11
Arun Richard Chandrasekaran
The development of molecular electronics is one of the current focuses of bottom-up nanotechnology. DNA has been the building block for nanostructures with a variety of applications, with its use extended to the formation of conducting nanowires. The one-dimensional silver/DNA hybrid arrays reported recently is a step towards achieving longer DNA nanowires.
August 3, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28754968/dna-self-assembly-catalyzed-by-artificial-agents
#12
Chao Shi, Yifan Wang, Menghua Zhang, Cuiping Ma
Nucleic acids have been shown to be versatile molecules and engineered to produce various nanostructures. However, the poor rate of these uncatalyzed nucleic acid reactions has restricted the development and applications. Herein, we reported a novel finding that DNA self-assembly could be nonenzymatically catalyzed by artificial agents with an increasing dissociation rate constant K2. The catalytic role of several artificial agents in DNA self-assembly was verified by real-time fluorescent detection or agarose gel electrophoresis...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28754940/a-device-that-operates-within-a-self-assembled-3d-dna-crystal
#13
Yudong Hao, Martin Kristiansen, Ruojie Sha, Jens J Birktoft, Carina Hernandez, Chengde Mao, Nadrian C Seeman
Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system...
August 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28752173/improved-i-motif-thermal-stability-by-insertion-of-anthraquinone-monomers
#14
Alaa S Gouda, Mahasen S Amine, Erik B Pedersen
In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone...
August 9, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28750513/a-dna-walker-as-a-fluorescence-signal-amplifier
#15
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...
August 7, 2017: Nano Letters
https://www.readbyqxmd.com/read/28731332/tuning-the-cavity-size-and-chirality-of-self-assembling-3d-dna-crystals
#16
Chad R Simmons, Fei Zhang, Tara MacCulloch, Noureddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C Seeman, Hao Yan
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28730451/using-planar-phi29-prna-three-way-junction-to-control-size-and-shape-of-rna-nanoparticles-for-biodistribution-profiling-in-mice
#17
Farzin Haque, Congcong Xu, Daniel L Jasinski, Hui Li, Peixuan Guo
RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730435/supported-fluid-lipid-bilayer-as-a-scaffold-to-direct-assembly-of-rna-nanostructures
#18
Aleksandra P Dabkowska, Agnes Michanek, Luc Jaeger, Arkadiusz Chworos, Tommy Nylander, Emma Sparr
RNA architectonics offers the possibility to design and assemble RNA into specific shapes, such as nanoscale 3D solids or nanogrids. Combining the minute size of these programmable shapes with precise positioning on a surface further enhances their potential as building blocks in nanotechnology and nanomedicine. Here we describe a bottom-up approach to direct the arrangement of nucleic acid nanostructures by using a supported fluid lipid bilayer as a surface scaffold. The strong attractive electrostatic interactions between RNA polyanions and cationic lipids promote RNA adsorption and self-assembly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#19
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#20
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
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