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Dna origami

Jianbang Wang, Zhixin Zhou, Liang Yue, Shan Wang, Itamar Willner
The switchable reconfiguration of a mixture of two dimers of DNA origami tiles AB and CD into a mixture of two DNA origami dimers composed of AD and CB, using collection of fuel and anti-fuel strands, is presented. The reversible reconfiguration of the mixture of dimers AB/CD into AD/CB followed by labeling each of the tile with 0, 1, 2 and 3 4× hairpins labels and by imaging the dimer structures by AFM. Subjecting the reconfigurable dimer mixtures to a collection of Mg2+ -dependent DNAzyme subunits and the substrates consisting of the ROX/BHQ2-modified substrate and the FAM/BHQ1-modified substrate leads to the triggered and programmed switchable operation in the presence of appropriate fuel and anti-fuel strands...
March 14, 2018: Nano Letters
Ennio Tasciotti
No abstract text is available yet for this article.
March 6, 2018: Nature Biotechnology
Philip Ketterer, Adithya N Ananth, Diederik S Laman Trip, Ankur Mishra, Eva Bertosin, Mahipal Ganji, Jaco van der Torre, Patrick Onck, Hendrik Dietz, Cees Dekker
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant...
March 2, 2018: Nature Communications
Caroline Hartl, Kilian Frank, Heinz Amenitsch, Stefan Fischer, Tim Liedl, Bert Nickel
DNA origami objects allow for accurate positioning of guest molecules in three dimensions. Validation and understanding of design strategies for particle attachment as well as analysis of specific particle arrangements are desirable. Small-angle X-ray scattering (SAXS) is suited to probe distances of nano-objects with sub-nanometer resolution at physiologically relevant conditions including pH and salt, and at varying temperatures. Here we show that the pair density distribution function (PDDF) obtained from an indirect Fourier transform of SAXS intensities in a model-free way allows to investigate prototypical DNA origami-mediated gold nanoparticle (AuNP) assemblies...
March 2, 2018: Nano Letters
Yu Tokura, Sean Harvey, Xuemei Xu, Chaojian Chen, Svenja Morsbach, Katrin Wunderlich, George Fytas, Yuzhou Wu, David Y W Ng, Tanja Weil
We describe the stepwise synthesis of precise polymeric objects programmed by a 3D DNA tube transformed from a common 2D DNA tile as a precise biotemplate for atom transfer radical polymerization. The catalytic interior space of the DNA tube was utilized for synthesizing a bio-inspired polymer, polydopamine.
March 1, 2018: Chemical Communications: Chem Comm
Henri G Franquelim, Alena Khmelinskaia, Jean-Philippe Sobczak, Hendrik Dietz, Petra Schwille
Membrane sculpting and transformation is essential for many cellular functions, thus being largely regulated by self-assembling and self-organizing protein coats. Their functionality is often encoded by particular spatial structures. Prominent examples are BAR domain proteins, the 'banana-like' shapes of which are thought to aid scaffolding and membrane tubulation. To elucidate whether 3D structure can be uncoupled from other functional features of complex scaffolding proteins, we hereby develop curved DNA origami in various shapes and stacking features, following the presumable design features of BAR proteins, and characterize their ability for membrane binding and transformation...
February 23, 2018: Nature Communications
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
Suping Li, Qiao Jiang, Shaoli Liu, Yinlong Zhang, Yanhua Tian, Chen Song, Jing Wang, Yiguo Zou, Gregory J Anderson, Jing-Yan Han, Yung Chang, Yan Liu, Chen Zhang, Liang Chen, Guangbiao Zhou, Guangjun Nie, Hao Yan, Baoquan Ding, Yuliang Zhao
Nanoscale robots have potential as intelligent drug delivery systems that respond to molecular triggers. Using DNA origami we constructed an autonomous DNA robot programmed to transport payloads and present them specifically in tumors. Our nanorobot is functionalized on the outside with a DNA aptamer that binds nucleolin, a protein specifically expressed on tumor-associated endothelial cells, and the blood coagulation protease thrombin within its inner cavity. The nucleolin-targeting aptamer serves both as a targeting domain and as a molecular trigger for the mechanical opening of the DNA nanorobot...
March 2018: Nature Biotechnology
Xiao Wang, Chen Li, Dong Niu, Ruojie Sha, Nadrian C Seeman, James W Canary
An electro-optical modulator was constructed using a DNA nanostructure scaffold with oligomers of poly(phenylene vinylene) and polyaniline. A molecular device containing one each of the functional molecules was assembled in a DNA origami. The constructs formed an "X" shape and were visualized by AFM. In response to redox reconfiguration, the device reversibly altered fluorescence signal output. This molecular self-assembly strategy provides opportunities to make unique material composites that are difficult to achieve by blending...
February 12, 2018: Nano Letters
Elisa Alina Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah Elisabeth Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, Ulrich F Keyser
We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nano-devices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labelled with a single pair of FRET dyes. The DNA structures were reversibly immobilised on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency...
February 12, 2018: Nano Letters
Dongsheng Lei, Alexander E Marras, Jianfang Liu, Chao-Min Huang, Lifeng Zhou, Carlos E Castro, Hai-Jun Su, Gang Ren
Scaffolded DNA origami has proven to be a powerful and efficient technique to fabricate functional nanomachines by programming the folding of a single-stranded DNA template strand into three-dimensional (3D) nanostructures, designed to be precisely motion-controlled. Although two-dimensional (2D) imaging of DNA nanomachines using transmission electron microscopy and atomic force microscopy suggested these nanomachines are dynamic in 3D, geometric analysis based on 2D imaging was insufficient to uncover the exact motion in 3D...
February 9, 2018: Nature Communications
Boxuan Shen, Veikko Linko, Kosti Tapio, Siim Pikker, Tibebe Lemma, Ashwin Gopinath, Kurt V Gothelf, Mauri A Kostiainen, J Jussi Toppari
Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties...
February 2018: Science Advances
Chanseok Lee, Jae Young Lee, Do-Nyun Kim
The originally published version of this Article contained an error in Figure 5. In panel f, the right y-axis 'Strain energy (kbT)' was labelled 'Probability' and the left y-axis 'Probability' was labelled 'Strain energy (kbT)'. This error has now been corrected in both the PDF and HTML versions of the Article.
February 7, 2018: Nature Communications
Jonathan R Burns, Baptiste Lamarre, Alice L B Pyne, James E Noble, Maxim G Ryadnov
A synthetic topology for everted viruses is reported. The topology is a single-stranded virion DNA assembled into a hollow cube with exterior decorated with HIV-Tat transduction domains. The cube incorporates a pH-responsive lid allowing for the controlled encapsulation of functional proteins and their transfer and release into live cells. Unlike viruses, which are protein shells with a [3,5]-fold rotational symmetry that encase nucleic acids, these cubes are [3, 4]-fold DNA boxes encapsulating proteins. Like viruses, such everted DNA-built viruses are monodisperse nanoscale assemblies that infect human cells with a specialist cargo...
February 9, 2018: ACS Synthetic Biology
Shuo Yang, Wenyan Liu, Rachel Nixon, Risheng Wang
We present a novel metal-ion stimulated organization of DNA origami nanostructures by employing G-quadruplexes as stimuli-responsive bridges. The reversible assembly process of DNA origami was the result of conformational changes between the G-quadruplex and its single-strand state induced by monovalent cations. This study might stimulate a new design of responsive DNA-based intelligent nanomaterials.
February 7, 2018: Nanoscale
Marco S L Tang, Simon Chi-Chin Shiu, Maia Godonoga, Yee-Wai Cheung, Shaolin Liang, Roderick M Dirkzwager, Andrew B Kinghorn, Lewis A Fraser, Jonathan G Heddle, Julian A Tanner
DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. Whilst DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase...
January 30, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
Pengfei Wang, Mohammad Aminur Rahman, Zhixiang Zhao, Kristin Weiss, Chao Zhang, Zhengjia Chen, Selwyn J Hurwitz, Zhuo G Chen, Dong M Shin, Yonggang Ke
DNA origami is a promising molecular delivery system for a variety of therapeutic applications including cancer therapy, given its capability to fabricate homogeneous nanostructures whose physicochemical properties (size, shape, surface chemistry) can be precisely tailored. However, the correlation between DNA-origami design and internalization efficiency in different cancer cell lines remains elusive. We investigated the cellular uptake of four DNA-origami nanostructures (DONs) with programmed sizes and shapes in multiple human cancer cell lines...
February 6, 2018: Journal of the American Chemical Society
Fabio Lapenta, Jana Aupič, Žiga Strmšek, Roman Jerala
The design of new protein folds represents a grand challenge for synthetic, chemical and structural biology. Due to the good understanding of the principles governing its pairing specificity, coiled coil (CC) peptide secondary structure elements can be exploited for the construction of modular protein assemblies acting as a proxy for the straightforward complementarity of DNA modules. The prerequisite for the successful translation of the modular assembly strategy pioneered by DNA nanotechnology to protein design is the availability of orthogonal building modules: a collection of peptides that assemble into CCs only with their predetermined partners...
February 5, 2018: Chemical Society Reviews
Yuezhou Zhang, Jing Tu, Dongqing Wang, Haitao Zhu, Sajal Kumar Maity, Xiangmeng Qu, Bram Bogaert, Hao Pei, Hongbo Zhang
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures...
February 1, 2018: Advanced Materials
Na Liu, Tim Liedl
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has established itself as a discipline, where near-field effects of electromagnetic waves created in the vicinity of metallic surfaces can give rise to a variety of novel phenomena and fascinating applications. As research on plasmonics has emerged from the optics and solid-state communities, most laboratories employ top-down lithography to implement their nanophotonic designs...
January 31, 2018: Chemical Reviews
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