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Dna origami

Mahsa Siavashpouri, Christian H Wachauf, Mark J Zakhary, Florian Praetorius, Hendrik Dietz, Zvonimir Dogic
Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch...
May 22, 2017: Nature Materials
Qingshan Wei, Guillermo Acuna, Seungkyeum Kim, Carolin Vietz, Derek Tseng, Jongjae Chae, Daniel Shir, Wei Luo, Philip Tinnefeld, Aydogan Ozcan
Smartphone fluorescence microscopy has various applications in point-of-care (POC) testing and diagnostics, ranging from e.g., quantification of immunoassays, detection of microorganisms, to sensing of viruses. An important need in smartphone-based microscopy and sensing techniques is to improve the detection sensitivity to enable quantification of extremely low concentrations of target molecules. Here, we demonstrate a general strategy to enhance the detection sensitivity of a smartphone-based fluorescence microscope by using surface-enhanced fluorescence (SEF) created by a thin metal-film...
May 18, 2017: Scientific Reports
Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy...
June 2017: Nature Protocols
Ivana Domljanovic, Annika Carstens, Anders Okholm, Jørgen Kjems, Christoffer Tandrup Nielsen, Niels H H Heegaard, Kira Astakhova
To date, there are multiple assays developed that detect and quantify antibodies in biofluids. Nevertheless, there is still a lack of simple approaches that specifically detect autoimmune antibodies to double-stranded DNA. Herein we investigate the potential of novel nucleic acid complexes as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA...
May 15, 2017: Scientific Reports
Dianming Wang, Yiyang Zhang, Dongsheng Liu
Transmembrane proteins are mostly nanochannels playing a highly important role in metabolism. Understanding their structures and functions is vital for revealing life processes. It is of fundamental interest to develop chemical devices to mimic biological channels. Structural DNA nanotechnology has been proven to be a promising method for the preparation of fine DNA nanochannels as a result of the excellent properties of DNA molecules. This review presents the development history and current situation of three different types of DNA nanochannel: tile-based nanotube, DNA origami nanochannel, and DNA bundle nanochannel...
2017: F1000Research
Keyao Pan, William P Bricker, Sakul Ratanalert, Mark Bathe
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5-100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost...
May 8, 2017: Nucleic Acids Research
Ken Halvorsen, Megan E Kizer, Xing Wang, Arun Richard Chandrasekaran, Maria Basanta-Sanchez
As DNA nanotechnology matures, there is increasing need for fast, reliable, and automated purification methods. Here, we develop UHPLC methods to purify self-assembled DNA nanoswitches, which are formed using DNA origami approaches and are designed to change conformations in response to a binding partner. We found that shear degradation hindered LC purification of the DNA nanoswitches, removing oligonucleotides from the scaffold strand and causing loss of function. However, proper choice of column, flow rate, and buffers enabled robust and automated purification of DNA nanoswitches without loss of function in under a half hour...
May 8, 2017: Analytical Chemistry
Bing Liu, Chunyuan Song, Dan Zhu, Xu Wang, Mengzhen Zhao, Yanjun Yang, Yinan Zhang, Shao Su, Jiye Shi, Jie Chao, Huajie Liu, Yun Zhao, Chunhai Fan, Lianhui Wang
Precise control over the assembly of anisotropic plasmonic gold nanostructures with relative spatial directionality and sequence asymmetry remains a major challenge and offers great fundamental insight and optical application possibilities. Here, a novel strategy is developed to anisotropically functionalize gold nanorods (AuNRs) by using a DNA-origami-based precise machine to transfer essential DNA sequence configurations to the surface of the AuNRs through an intentionally designed toehold-initiated displacement reaction...
April 27, 2017: Small
Sarit S Agasti, Yu Wang, Florian Schueder, Aishwarya Sukumar, Ralf Jungmann, Peng Yin
Recent advances in super-resolution fluorescence imaging allow researchers to overcome the classical diffraction limit of light, and are already starting to make an impact in biology. However, a key challenge for traditional super-resolution methods is their limited multiplexing capability, which prevents a systematic understanding of multi-protein interactions on the nanoscale. Exchange-PAINT, a recently developed DNA-based multiplexing approach, in theory facilitates spectrally-unlimited multiplexing by sequentially imaging target molecules using orthogonal dye-labeled 'imager' strands...
April 1, 2017: Chemical Science
Carolin Vietz, Izabela Kaminska, Maria Sanz Paz, Philip Tinnefeld, Guillermo P Acuna
Plasmonic structures are known to affect the fluorescence properties of dyes placed in close proximity. This effect has been exploited in combination with single-molecule techniques for several applications in the field of biosensing. Among these plasmonic structures, top-down zero-mode waveguides stand out due to their broadband capabilities. In contrast, optical antennas based on gold nanostructures exhibit fluorescence enhancement on a narrow fraction of the visible spectrum typically restricted to the red to near-infrared region...
April 28, 2017: ACS Nano
Yuwei Hu, Alessandro Cecconello, Andrea Idili, Francesco Ricci, Itamar Willner
Triplex nucleic acids attract recent interest as part of the rich "tool-box" of structures used to develop DNA-based nanostructures and materials. This review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles and the reversible oligomerization of "origami" tiles or DNA circles are described. Also, the use of triplex-DNA structures as functional units to assemble pH-responsive systems and materials are presented...
April 26, 2017: Angewandte Chemie
Jerzy Kozyra, Alessandro Ceccarelli, Emanuela Torelli, Annunziata Lopiccolo, Jing-Ying Gu, Harold Fellermann, Ulrich Stimming, Natalio Krasnogor
Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding...
April 25, 2017: ACS Synthetic Biology
Gabriella Marth, Andrew M Hartley, Samuel C Reddington, Lauren L Sargisson, Marlène Parcollet, Katherine E Dunn, D Dafydd Jones, Eugen Stulz
We demonstrate an approach that allows attachment of single-stranded DNA (ssDNA) to a defined residue in a protein of interest (POI) so as to provide optimal and well-defined multicomponent assemblies. Using an expanded genetic code system, azido-phenylalanine (azF) was incorporated at defined residue positions in each POI; copper-free click chemistry was used to attach exactly one ssDNA at precisely defined residues. By choosing an appropriate residue, ssDNA conjugation had minimal impact on protein function, even when attached close to active sites...
April 20, 2017: ACS Nano
Karen B Ricardo, Anqin Xu, Muhammad Salim, Feng Zhou, Haitao Liu
We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO2...
April 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Toma E Tomov, Roman Tsukanov, Yair Glick, Yaron Berger, Miran Liber, Dorit Avrahami, Doron Gerber, Eyal Nir
Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines...
April 25, 2017: ACS Nano
Honglu Zhang, Jie Chao, Dun Pan, Huajie Liu, Yu Qiang, Ke Liu, Chengjun Cui, Jianhua Chen, Qing Huang, Jun Hu, Lianhui Wang, Wei Huang, Yongyong Shi, Chunhai Fan
Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms...
April 6, 2017: Nature Communications
Prakash Shrestha, Sagun Jonchhe, Tomoko Emura, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, Hanbin Mao
Molecular simulations suggest that the stability of a folded macromolecule increases in a confined space due to entropic effects. However, due to the interactions between the confined molecular structure and the walls of the container, clear-cut experimental evidence for this prediction is lacking. Here, using DNA origami nanocages, we show the pure effect of confined space on the property of individual human telomeric DNA G-quadruplexes. We induce targeted mechanical unfolding of the G-quadruplex while leaving the nanocage unperturbed...
March 27, 2017: Nature Nanotechnology
Masudur Rahman, David Neff, Nathaniel Green, Michael L Norton
Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite...
October 31, 2016: Nanomaterials
Boxuan Shen, Kosti Tapio, Veikko Linko, Mauri A Kostiainen, Jari Jussi Toppari
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds...
August 10, 2016: Nanomaterials
E-C Schöneweiß, B Saccà
Dynamic DNA nanotechnology relies on the integration of small switchable motifs at suitable positions of DNA nanostructures, thus enabling the manipulation of matter with nanometer spatial accuracy in a trigger-dependent fashion. Typical examples of such motifs are hairpins, whose elongation into duplexes can be used to perform long-range, translational movements. In this work, we used temperature-dependent FRET spectroscopy to determine the thermal stabilities of distinct sets of hairpins integrated into the central seam of a DNA origami structure...
March 20, 2017: Nanoscale
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