keyword
MENU ▼
Read by QxMD icon Read
search

Dna origami

keyword
https://www.readbyqxmd.com/read/28808731/biomacromolecules-as-tools-and-objects-in-nanometrology-current-challenges-and-perspectives
#1
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
#2
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
#3
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/28745060/tunable-fluorescence-of-a-semiconducting-polythiophene-positioned-on-dna-origami
#4
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
#5
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
#6
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...
July 24, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28734728/a-new-ppar%C3%AE-dna-origami-biochromatography-and-offline-high-performance-liquid-chromatography-mass-spectrometry-method-for-screening-ppar%C3%AE-receptor-antagonists-from-ginsenosides
#7
Jie Zhou, Chong Sun, Lingchang Meng, Weiran Ye, Pei Luo, Fang Sun, Shanshan Chen, Xia Xu
To rapidly identify novel PPARγ ligands, a robust binding assay amenable to high-efficiency screening toward PPARγ would be desirable. In this study, a new PPARγ assembled on DNA origami (PPARγ/DNA origami) biochromatography drug screening model was constructed and evaluated. The method was used to screen active ingredients acted on PPARγ from the total ginsenosides. The total ginsenosides were handled on this biochromatography column by HPLC. The collected retention fraction from the biochromatography column was analyzed by HPLC and HPLC/MS...
September 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28714559/how-we-make-dna-origami
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28650478/a-dna-origami-platform-for-quantifying-protein-copy-number-in-super-resolution
#18
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...
August 2017: Nature Methods
https://www.readbyqxmd.com/read/28639303/an-addressable-2d-heterogeneous-nanoreactor-to-study-the-enzyme-catalyzed-reaction-at-the-interface
#19
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
#20
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
keyword
keyword
116895
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"