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Dna origami

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https://www.readbyqxmd.com/read/27903819/towards-designing-new-nano-scale-protein-architectures
#1
REVIEW
Jana Aupič, Fabio Lapenta, Žiga Strmšek, Roman Jerala
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27893729/programmable-disorder-in-random-dna-tilings
#2
Grigory Tikhomirov, Philip Petersen, Lulu Qian
Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network-random loops, mazes and trees-on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution...
November 28, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27893728/dna-origami-tiles-nanoscale-mazes
#3
Fei Zhang, Fan Hong, Hao Yan
No abstract text is available yet for this article.
November 28, 2016: Nature Nanotechnology
https://www.readbyqxmd.com/read/27890616/cerium-chloride-stimulated-controlled-conversion-of-b-to-z-dna-in-self-assembled-nanostructures
#4
Madhabi M Bhanjadeo, Ashok K Nayak, Umakanta Subudhi
DNA adopts different conformation not only because of novel base pairs but also while interacting with inorganic or organic compounds. Dynamic origami or self-assembled branched DNA (bDNA) structures that change conformation in response to environmental cues hold great promises in sensing and actuation at the nanoscale. Recently, the B-Z transition in DNA is being explored to design various nanomechanical devices. In this communication we have demonstrated that Cerium chloride binds to the phosphate backbone of self-assembled bDNA structure and induce B-to-Z transition at physiological concentration...
November 24, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27869278/cellular-delivery-of-enzyme-loaded-dna-origami
#5
Ari Ora, Erika Järvihaavisto, Hongbo Zhang, Henni Auvinen, Hélder A Santos, Mauri A Kostiainen, Veikko Linko
In this communication, we show that active enzymes can be delivered into HEK293 cells in vitro when they are attached to tubular DNA origami nanostructures. We use bioluminescent enzymes as a cargo and monitor their activity from a cell lysate. The results show that the enzymes stay intact and retain their activity in the transfection process. The method is highly modular, which makes it a compelling candidate for a great variety of delivery applications.
December 1, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27846560/molecular-force-spectroscopy-with-a-dna-origami-based-nanoscopic-force-clamp
#6
Philipp C Nickels, Bettina Wünsch, Phil Holzmeister, Wooli Bae, Luisa M Kneer, Dina Grohmann, Philip Tinnefeld, Tim Liedl
Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer...
October 21, 2016: Science
https://www.readbyqxmd.com/read/27829617/mechano-nanoarchitectonics-for-bio-functions-at-interfaces
#7
Katsuhiko Ariga
Architecting well-designed interfacial structures is crucial for fabrication of better bio-related devices such as bio-sensors. A dynamic nature of the interfacial structures with appropriate mechanical properties is advantageous for interactions with bio-related substances. In this short review, a new term, mechano-nanoarchitectonics, has been proposed. This terminology represents nanoarchitectonics methodology for formation of functional structures and regulation of their properties with the aid of mechanical processes...
2016: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/27821763/design-of-a-molecular-support-for-cryo-em-structure-determination
#8
Thomas G Martin, Tanmay A M Bharat, Andreas C Joerger, Xiao-Chen Bai, Florian Praetorius, Alan R Fersht, Hendrik Dietz, Sjors H W Scheres
Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air-water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27813014/a-proximity-based-programmable-dna-nanoscale-assembly-line
#9
Xiaoyan Zhang, Xiaoqiang Ding, Jianzhou Zou, Hongzhou Gu
The assembly line is one of the key features of industrial production on the macroscopic scale, allowing programmability and sequential addition of parts to a final product. In this chapter, we use DNA to extend this notion to the nanoscale by the judicious combination of three DNA-based components: a DNA origami tile that provides a framework and track for the assembly process, three two-state DNA cassettes that can be programmed to donate cargo and are attached to the tile, and a DNA walker that can move on the track to collect cargo...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813012/confined-growth-of-metal-nanoparticles-within-3d-dna-origami-molds
#10
Wei Sun, Jie Shen
Manufacturing prescribed shaped metal nanoparticles promises emerging applications in plasmonics, energy, and disease diagnosis. The key to the shape-controllable synthesis is generating local environments encoded with prescribed geometrical information. Here, we describe a general strategy that uses 3D self-assembled DNA origami as mold to confine the casting growth of metal nanoparticle. By transferring the shape information from DNA cavities to metal nanoparticles, metal nanoparticles with prescribed shapes, dimensions, and surface binding features could be rationally designed and synthesized...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813008/lipid-membrane-encapsulation-of-a-3d-dna-nano-octahedron
#11
Steven D Perrault, William M Shih
Structural DNA nanotechnology methods such as DNA origami allow for the synthesis of highly precise nanometer-scale materials (Rothemund, Nature 440:297-302, 2006; Douglas et al., Nature 459:414-418, 2009). These offer compelling advantages for biomedical applications. Such materials can suffer from structural instability in biological environments due to denaturation and nuclease digestion (Hahn et al., ACS Nano 2014; Perrault and Shih, ACS Nano 8:5132-5140, 2014). Encapsulation of DNA nanostructures in a lipid membrane compartmentalizes them from their environment and prevents denaturation and nuclease digestion (Perrault and Shih, ACS Nano 8:5132-5140, 2014)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813007/spatial-organization-of-enzyme-cascade-on-a-dna-origami-nanostructure
#12
Jinglin Fu, Tianran Li
Self-assembled DNA nanostructures hold great promise to organize multi-enzyme systems with the precise control of the geometric arrangements. Enzymes modified with single-stranded DNA anchors are assembled onto the DNA origami tiles by hybridizing with the corresponding complementary strands displayed on the surface of the DNA nanostructures. Here, we describe a protocol of assembling a two-enzyme cascade on a discrete, rectangular DNA origami tile, where the distance between enzymes is precisely controlled for investigating the distance-dependent cascade activities...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27813001/computer-aided-design-of-rna-origami-structures
#13
Steffen L Sparvath, Cody W Geary, Ebbe S Andersen
RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27802042/3d-dna-origami-cuboids-as-monodisperse-patchy-nanoparticles-for-switchable-hierarchical-self-assembly
#14
Thomas Tigges, Thomas Heuser, Rahul Tiwari, Andreas Walther
The rational design of anisotropic interaction patterns is a key step for programming colloid and nanoparticle self-assembly and emergent functions. Herein, we demonstrate a concept for harnessing the capabilities of 3D DNA origami for extensive supracolloidal self-assembly, and showcase its use for making truly monodisperse, patchy, divalent nanocuboids that can self-assemble into supracolloidal fibrils via programmable DNA hybridization. A change in the number of connector duplexes at the patches reveals that multivalency and cooperativity play crucial roles to enhance superstructure formation...
November 1, 2016: Nano Letters
https://www.readbyqxmd.com/read/27779405/regular-nanoscale-protein-patterns-via-directed-adsorption-through-self-assembled-dna-origami-masks
#15
Saminathan Ramakrishnan, Sivaraman Subramaniam, Adrian Francis Stewart, Guido Grundmeier, Adrian Keller
DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas...
October 25, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27748519/specific-growth-rate-and-multiplicity-of-infection-affect-high-cell-density-fermentation-with-bacteriophage-m13-for-ssdna-production
#16
Benjamin Kick, Samantha Hensler, Florian Praetorius, Hendrik Dietz, Dirk Weuster-Botz
The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection and specific growth rate...
October 17, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27718534/cargo-rigidity-affects-the-sensitivity-of-dynein-ensembles-to-individual-motor-pausing
#17
Amalia R Driller-Colangelo, Karen W L Chau, Jessica M Morgan, Nathan D Derr
Cytoplasmic dynein is a minus-end directed microtubule-based motor protein that drives intracellular cargo transport in eukaryotic cells. Although many intracellular cargos are propelled by small groups of dynein motors, the biophysical mechanisms governing ensemble motility remain largely unknown. To investigate the emergent motility of motor ensembles, we have designed a programmable DNA origami synthetic cargo "chassis" enabling us to control the number of dynein motors in the ensemble and vary the rigidity of the cargo chassis itself...
October 8, 2016: Cytoskeleton
https://www.readbyqxmd.com/read/27709924/torsional-constraints-of-dna-substrates-impact-cas9-cleavage
#18
Michael H Räz, Kumi Hidaka, Shana J Sturla, Hiroshi Sugiyama, Masayuki Endo
To examine the effect of the torsional constraints imposed on DNA substrates on Cas9 cleavage, we prepared con-strained DNA substrates using a DNA origami frame. By fixing the dsDNA at the connectors of the DNA frame, we created four different dsDNA substrates containing torsion-ally constrained or relaxed strands. We quantified the cleav-age of constrained and relaxed substrates by Cas9 with quantitative PCR. Moreover, we observed the Cas9/sgRNA complex bound to the DNA substrates and characterized the dissociation of the complex with high-speed AFM...
October 6, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27689681/gold-nanorods-dna-origami-and-porous-silicon-nanoparticle-functionalized-biocompatible-double-emulsion-for-versatile-targeted-therapeutics-and-antibody-combination-therapy
#19
Feng Kong, Hongbo Zhang, Xiangmeng Qu, Xu Zhang, Dong Chen, Ruihua Ding, Ermei Mäkilä, Jarno Salonen, Hélder A Santos, Mingtan Hai
Gold nanorods, DNA origami, and porous silicon nanoparticle-functionalized biocompatible double emulsion are developed for versatile molecular targeted therapeutics and antibody combination therapy. This advanced photothermal responsive all-in-one biocompatible platform can be easily formed with great therapeutics loading capacity for different cancer treatments with synergism and multidrug resistance inhibition, which has great potential in advancing biomedical applications.
September 30, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27679425/dna-nanostructure-gold-nanorod-hybrids-for-enhanced-in-vivo-optoacoustic-imaging-and-photothermal-therapy
#20
Yang Du, Qiao Jiang, Nicolas Beziere, Linlin Song, Qian Zhang, Dong Peng, Chongwei Chi, Xin Yang, Hongbo Guo, Gaël Diot, Vasilis Ntziachristos, Baoquan Ding, Jie Tian
A functional cancer theranostic nanoplatform is developed, specifically tailored toward the optoacoustic modality by combining gold nanorods with DNA nanostructures (D-AuNR). DNA origami is used as an efficient delivery vehicle owing to its prominent tumor-targeting property. The D-AuNR hybrids display an enhanced tumor diagnostic sensitivity by improved optoacoustic imaging and excellent photothermal therapeutic properties in vivo.
December 2016: Advanced Materials
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