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Dna origami

Andreas Sprengel, Pascal Lill, Pierre Stegemann, Kenny Bravo-Rodriguez, Elisa-C Schöneweiß, Melisa Merdanovic, Daniel Gudnason, Mikayel Aznauryan, Lisa Gamrad, Stephan Barcikowski, Elsa Sanchez-Garcia, Victoria Birkedal, Christos Gatsogiannis, Michael Ehrmann, Barbara Saccà
The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA-protein conjugation still limit true emulation of natural host-guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA-protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action...
February 16, 2017: Nature Communications
Mike Heilemann, Franziska Fricke, Christos Karathanasis, Gerhard Hummer
Single-molecule localization microscopy (SMLM) can be used to count fluorescently labeled molecules even when they are not individually resolved. We demonstrate SMLM molecule counting for nucleic acids labeled with the organic fluorophore Alexa Fluor 647 and imaged under photoswitching conditions. From the observed distributions of the number of fluorophore blinking events, we extracted the number of fluorophores per spot using a statistical model. We validate the molecule counting method for single Alexa Fluor 647 fluorophores, and for trimers of Alexa Fluor 647 constructed on a DNA origami structure...
February 14, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Alessandro Angelin, Olivier Kassel, Sepand Rastegar, Uwe Strähle, Christof M Niemeyer
The unique structure-directing properties of DNA origami nanostructures (DONs) show great potential to specifically manipulate intracellular processes. We report an innovative concept to selectively activate the transcription of a single gene in the developing zebrafish embryo. We reason that engineering a designer transcription factor in which a rigid DON imposes a fixed distance between the DNA-binding domain (DBD) and the transactivation domain (TAD) would allow the selective activation of a gene harboring the same distance between the corresponding transcription factor binding site and the core promoter...
February 2017: ChemistryOpen
Jonas J Funke, Philip Ketterer, Corinna Lieleg, Sarah Schunter, Philipp Korber, Hendrik Dietz
Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions...
November 2016: Science Advances
Haorong Chen, Ruixin Li, Shiming Li, Joakim Andréasson, Jong Hyun Choi
The responses of DNA origami conformation to UV radiation of different wavelengths and doses are investigated. Short- and medium-wavelength UV light can cause photo-lesions in DNA origami. At moderate doses, the lesions do not cause any visible defects in the origami, nor do they significantly affect the hybridization capability. Instead, they help relieve the internal stress in the origami structure and restore it to the designed conformation. At high doses, staple dissociation increases which causes structural disintegration...
February 1, 2017: Journal of the American Chemical Society
Oscar Mendoza, Said Houmadi, Jean-Pierre Aimé, Juan Elezgaray
Logic circuits based on DNA strand displacement reaction are the basic building blocks of future nanorobotic systems. The circuits tethered to DNA origami platforms present several advantages over solution-phase versions where couplings are always diffusion-limited. Here we consider a possible implementation of one of the basic operations needed in the design of these circuits, namely, signal replication. We show that with an appropriate preparation of the initial state, signal replication performs in a reproducible way...
January 14, 2017: Journal of Chemical Physics
Bibek Uprety, Tyler Westover, Michael Stoddard, Kamron Brinkerhoff, John Jensen, Robert C Davis, Adam T Woolley, John N Harb
An improved method for the metallization of DNA origami is examined in this work. DNA origami, a simple and robust method for creating a wide variety of nanostructured shapes and patterns, provides an enabling template for bottom-up fabrication of next-generation nanodevices. Selective metallization of these DNA templates is needed to make nanoelectronic devices. Here, we demonstrate a metallization process that uses gold nanorod seeds followed by anisotropic plating to provide improved morphology and greater control of the final metallized width of the structure...
January 11, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
J M Majikes, J A Nash, T H LaBean
Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2...
January 11, 2017: Nanoscale
Mario Raab, Carolin Vietz, Fernando Daniel Stefani, Guillermo Pedro Acuna, Philip Tinnefeld
Over the last decade, two fields have dominated the attention of sub-diffraction photonics research: plasmonics and fluorescence nanoscopy. Nanoscopy based on single-molecule localization offers a practical way to explore plasmonic interactions with nanometre resolution. However, this seemingly straightforward technique may retrieve false positional information. Here, we make use of the DNA origami technique to both control a nanometric separation between emitters and a gold nanoparticle, and as a platform for super-resolution imaging based on single-molecule localization...
January 11, 2017: Nature Communications
Isaac Gállego, Brendan Manning, Joan Daniel Prades, Mònica Mir, Josep Samitier, Ramon Eritja
Sub-10 nm lithography of DNA patterns is achieved using the DNA-origami stamping method. This new strategy utilizes DNA origami to bind a preprogrammed DNA ink pattern composed of thiol-modified oligonucleotides on gold surfaces. Upon denaturation of the DNA origami, the DNA ink pattern is exposed. The pattern can then be developed by hybridization with complementary strands carrying gold nanoparticles.
January 6, 2017: Advanced Materials
Pengfei Zhan, Palash K Dutta, Pengfei Wang, Gang Song, Mingjie Dai, Shu-Xia Zhao, Zhen-Gang Wang, Peng Yin, Wei Zhang, Baoquan Ding, Yonggang Ke
Distinct electromagnetic properties can emerge from the three-dimensional (3D) configuration of a plasmonic nanostructure. Furthermore, the reconfiguration of a dynamic plasmonic nanostructure, driven by physical or chemical stimuli, may generate a tailored plasmonic response. In this work, we constructed a 3D reconfigurable plasmonic nanostructure with controllable, reversible conformational transformation using bottom-up DNA self-assembly. Three gold nanorods (AuNRs) were positioned onto a reconfigurable DNA origami tripod...
January 9, 2017: ACS Nano
Nicole A Estrich, Armando Hernandez-Garcia, Renko de Vries, Thomas H LaBean
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc...
January 6, 2017: ACS Nano
Yuanchen Dong, Yuhe Renee Yang, Yiyang Zhang, Dianming Wang, Xixi Wei, Saswata Banerjee, Yan Liu, Zhongqiang Yang, Hao Yan, Dongsheng Liu
We describe the use of a frame-guided assembly (FGA) strategy to construct cuboid and dumbbell-shaped hetero-vesicles on DNA origami nanostructure scaffolds. These are achieved by varying the design of the DNA origami scaffolds that direct the distribution of the leading hydrophobic groups (LHG). By careful selection of LHGs, different types of amphiphiles (both polymer and small-molecule surfactants) were guided to form hetero-vesicles, demonstrating the versatility of the FGA strategy and its potential to construct asymmetric and dynamic hetero-vesicle assemblies with complex DNA nano-scaffolds...
December 30, 2016: Angewandte Chemie
Kilian Vogele, Jonathan List, Günther Pardatscher, Nolan B Holland, Friedrich C Simmel, Tobias Pirzer
Nanoscale plasmonic waveguides composed of metallic nanoparticles are capable of guiding electromagnetic energy below the optical diffraction limit. Signal feed-in and readout typically require the utilization of electronic effects or near-field optical techniques, whereas for their fabrication mainly lithographic methods are employed. Here we developed a switchable plasmonic waveguide assembled from gold nanoparticles (AuNPs) on a DNA origami structure that facilitates a simple spectroscopic excitation and readout...
December 27, 2016: ACS Nano
Simone Ciarella, Oleg Gang, Francesco Sciortino
We evaluate the phase diagram of a model of tetrameric particles where the arms of the tetrahedra are made by six hard cylinders. An interacting site is present on each one of the four vertices allowing the particles to form a bonded network. These model particles provide a coarse-grained but realistic representation of recently synthesised DNA origami tetrahedra. We show that the resulting network is sufficiently empty to allow for partial interpenetration and it is sufficiently flexible to avoid crystallisation (at least on the numerical time scale), satisfying both criteria requested for the observation of a liquid-liquid critical point in tetrahedrally coordinated particles...
December 2016: European Physical Journal. E, Soft Matter
Zhisong Lu, Ying Wang, Dan Xu, Lei Pang
A DNA origami-based platform for detecting aflatoxin B1 has been constructed with the assistance of aptamer probes and its complementary ssDNA-modified gold nanoparticles. This work may open new horizons for the application of DNA origami in the detection of a variety of small molecules.
December 23, 2016: Chemical Communications: Chem Comm
Amir Barati Farimani, Payam Dibaeinia, Narayana R Aluru
DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases...
December 22, 2016: ACS Applied Materials & Interfaces
Eli J Curry, Atta D Henoun, Albert N Miller, Thanh D Nguyen
Recently, there has been an emerging interest in controlling 3D structures and designing novel 3D shapes for drug carriers at nano- and micro-scales. Certain 3D shapes and structures of drug particles enable transportation of the drugs to desired areas of the body, allow drugs to target specific cells and tissues, and influence release kinetics. Advanced nano- and micro-manufacturing methods including 3D printing, photolithography-based processes, microfluidics and DNA origami have been developed to generate defined 3D shapes and structures for drug carriers...
January 2017: Therapeutic Delivery
Jonas J Funke, Philip Ketterer, Corinna Lieleg, Philipp Korber, Hendrik Dietz
We establish a DNA origami based tool for quantifying conformational equilibria of biomolecular assemblies as a function of environmental conditions. As first application, we employed the tool to study the salt-induced disassembly of nucleosome core particles. To extract binding constants and energetic penalties, we integrated nucleosomes in the spectrometer such that unwrapping of the nucleosomal template DNA, leading from bent to more extended states was directly coupled to the conformation of the spectrometer...
December 14, 2016: Nano Letters
Jing Yang, Shuoxing Jiang, Xiangrong Liu, Linqiang Pan, Cheng Zhang
In this study, an aptamer-substrate strategy is introduced to control programmable DNA origami pattern. Combined with DNA aptamer-substrate binding and DNAzyme-cutting, small DNA tiles were specifically controlled to fill into the predesigned DNA origami frame. Here, a set of DNA logic gates (OR, YES, and AND) are performed in response to the stimuli of adenosine triphosphate (ATP) and cocaine. The experimental results are confirmed by AFM imaging and time-dependent fluorescence changes, demonstrating that the geometric patterns are regulated in a controllable and programmable manner...
December 14, 2016: ACS Applied Materials & Interfaces
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