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Dna origami

Tao Zhang, Caroline Hartl, Kilian Frank, Amelie Heuer-Jungemann, Stefan Fischer, Philipp C Nickels, Bert Nickel, Tim Liedl
3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1...
May 18, 2018: Advanced Materials
Denis Selnihhin, Steffen Møller Sparvath, Søren Preus, Victoria Birkedal, Ebbe Sloth Andersen
Biosensors play increasingly important roles in many fields, from clinical diagnosis to environmental monitoring, and there is a growing need for cheap and simple analytical devices. DNA nanotechnology provides methods for the creation of sophisticated biosensors, however many of the developed DNA-based sensors are limited by cumbersome and time-consuming readouts involving advanced experimental techniques. Here we describe design, construction and characterization of an optical DNA origami nano-biosensor device exploiting arrays of precisely positioned organic fluorophores...
May 15, 2018: ACS Nano
Maartje Bastings, Frances Anastassacos, Nandhini Ponnuswamy, Franziska Leifer, Garry Cuneo, Chenxiang Lin, Donald E Ingber, Ju Hee Ryu, William M Shih
Designer nanoparticles with controlled shape and size are increasingly popular vehicles for therapeutic delivery due to their enhanced cell delivery performance. However, our ability to fashion nanoparticles has offered only limited control over these parameters. Structural DNA nanotechnology has an unparalleled ability to self-assemble three-dimensional nanostructures with near-atomic resolution features and thus, it offers an attractive platform for systematic exploration of the parameter space relevant to nanoparticle uptake by living cells...
May 14, 2018: Nano Letters
Katharina Brassat, Saminathan Ramakrishnan, Julius Bürger, Marcel Hanke, Mahnaz Doostdar, Jörg K N Lindner, Guido Grundmeier, Adrian Keller
DNA origami nanostructures are versatile substrates for the controlled arrangement of molecular capture sites with nanometer precision and thus have many promising applications in single-molecule bioanalysis. Here, we investigate the adsorption of DNA origami nanostructures in nanohole arrays which represent an important class of biosensors and may benefit from the incorporation of DNA origami-based molecular probes. Nanoholes with well-defined diameter that enable the adsorption of single DNA origami triangles are fabricated in Au films on Si wafers by nanosphere lithography...
May 13, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Miran Liber, Toma E Tomov, Roman Tsukanov, Yaron Berger, Mary Popov, Dinesh C Khara, Eyal Nir
Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted...
May 4, 2018: Small
Maximilian T Strauss, Florian Schueder, Daniel Haas, Philipp C Nickels, Ralf Jungmann
Self-assembled DNA nanostructures feature an unprecedented addressability with sub-nanometer precision and accuracy. This addressability relies on the ability to attach functional entities to single DNA strands in these structures. The efficiency of this attachment depends on two factors: incorporation of the strand of interest and accessibility of this strand for downstream modification. Here we use DNA-PAINT super-resolution microscopy to quantify both incorporation and accessibility of all individual strands in DNA origami with molecular resolution...
April 23, 2018: Nature Communications
Andreas Walther, Sebastian Loescher, Saskia Groeer
Scaffold-based lattice-engineered 3D DNA origami emerges as a powerful and versatile technique for the rational design and built-up of arbitrary and monodisperse DNA-based 3D nanoobjects. Relying on the unsurpassed molecular programmability of sequence-specific DNA hybridization, a long circular ssDNA strand (termed scaffold) is assembled with many short ssDNA oligomers (termed staples), which organize the scaffold into a 3D lattice in a single step leading to highest precision 3D nanoparticulate structures with high yields...
April 20, 2018: Angewandte Chemie
Florence Benn, Natalie E C Haley, Alexandra E Lucas, Emma Silvester, Seham Helmi, Robert Schreiber, Jonathan Bath, Andrew J Turberfield
We report the design and assembly of chiral DNA nanotubes with well-defined and addressable inside and outside surfaces. We demonstrate that the outside surface can be functionalised with a chiral arrangement of gold nanoparticles to create a plasmonic device and that the inside surface can be functionalised with a track for a molecular motor allowing transport of a cargo within the central cavity.
April 18, 2018: Angewandte Chemie
Jonas Mücksch, Philipp Blumhardt, Maximilian T Strauss, Eugene P Petrov, Ralf Jungmann, Petra Schwille
We present a simple and versatile single molecule-based method for the accurate determination of binding rates to surfaces or surface bound receptors. To quantify the reversible surface attachment of fluorescently labeled molecules, we have modified previous schemes for Fluorescence Correlation Spectroscopy with Total Internal Reflection illumination (TIR-FCS) and camera-based detection. In contrast to most modern applications of TIR-FCS, we completely disregard spatial information in lateral direction. Instead, we perform correlation analysis on a spatially integrated signal, effectively converting the illuminated surface area into the measurement volume...
April 16, 2018: Nano Letters
Yuki Suzuki, Masayuki Endo, Hiroshi Sugiyama
Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Here, we aimed to use the internal cavities of a preassembled two-dimensional (2D) DNA origami framework to incorporate supplemental square-shaped DNA origamis (SQ-origamis) with shapes that were complementary to those of the cavities. In our approach, the framework was first self-assembled on a mica-supported lipid bilayer membrane from cross-shaped DNA origamis (CR-origamis), and subsequently exposed to the SQ-origamis...
April 12, 2018: Angewandte Chemie
Michael W Grome, Zhao Zhang, Frédéric Pincet, Chenxiang Lin
A major goal of nanotechnology and bioengineering is to build artificial nanomachines capable of generating specific membrane curvatures on demand. Inspired by natural membrane-deforming proteins, here we design DNA-origami curls that polymerize into nanosprings and show their efficacy in vesicle deformation. DNA-coated membrane tubules emerge from spherical vesicles when DNA-origami polymerization or high membrane-surface coverage occurs. Unlike many previous methods, the DNA self-assembly-mediated membrane tubulation eliminates the need for detergent or top-down manipulation...
March 25, 2018: Angewandte Chemie
Christian Heck, Yuya Kanehira, Janina Kneipp, Ilko Bald
This study demonstrates the bottom-up synthesis of silver nanolenses. A robust coating protocol enabled the functionalization of differently-sized silver nanoparticles with DNA single strands of orthogonal sequence. Coated particles 10 nm, 20 nm, and 60 nm in diameter, respectively, were self-assembled by DNA origami scaffolds to form silver nanolenses. Single entities of the protein streptavidin were selectively integrated in the gap of highest electric field enhancement. Streptavidin labelled with alkyne groups served as model analyte in surface-enhanced Raman scattering (SERS) experiments...
March 25, 2018: Angewandte Chemie
Linda K Bruetzel, Philipp Walker, Thomas Gerling, Hendrik Dietz, Jan Lipfert
Self-assembled DNA structures enable creation of specific shapes at the nm-µm scale with molecular resolution. The creation of functional DNA assemblies will likely require dynamic structures that can undergo controllable conformational changes. DNA devices based on shape complementary stacking interactions have been demonstrated to undergo reversible conformational changes triggered by changes in ionic environment or temperature. An experimentally unexplored aspect is how quickly conformational transitions of large synthetic DNA origami structures can actually occur...
March 20, 2018: Nano Letters
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 subnanometer 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...
April 11, 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 13, 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...
March 27, 2018: ACS Nano
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