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Dna origami

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https://www.readbyqxmd.com/read/28414914/designing-uniquely-addressable-bio-orthogonal-synthetic-scaffolds-for-dna-and-rna-origami
#1
Jerzy W 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 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 optimised for high-yield folding...
April 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28414900/precision-templated-bottom-up-multiprotein-nanoassembly-through-defined-click-chemistry-linkage-to-dna
#2
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
https://www.readbyqxmd.com/read/28406032/deposition-of-dna-nanostructures-on-highly-oriented-pyrolytic-graphite
#3
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
https://www.readbyqxmd.com/read/28402651/dna-bipedal-motor-achieves-a-large-number-of-steps-due-to-operation-using-microfluidics-based-interface
#4
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 14, 2017: ACS Nano
https://www.readbyqxmd.com/read/28382928/dna-origami-based-shape-ids-for-single-molecule-nanomechanical-genotyping
#5
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
https://www.readbyqxmd.com/read/28346457/confined-space-facilitates-g-quadruplex-formation
#6
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
https://www.readbyqxmd.com/read/28335324/dna-origami-reorganizes-upon-interaction-with-graphite-implications-for-high-resolution-dna-directed-protein-patterning
#7
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
https://www.readbyqxmd.com/read/28335274/metallic-nanostructures-based-on-dna-nanoshapes
#8
REVIEW
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
https://www.readbyqxmd.com/read/28317958/the-collective-behavior-of-spring-like-motifs-tethered-to-a-dna-origami-nanostructure
#9
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
https://www.readbyqxmd.com/read/28295864/block-copolymer-micellization-as-a-protection-strategy-for-dna-origami
#10
Nayan P Agarwal, Michael Matthies, Fatih N Gür, Kensuke Osada, Thorsten L Schmidt
DNA nanotechnology enables the synthesis of nanometer-sized objects that can be site-specifically functionalized with a large variety of materials. For these reasons, DNA-based devices such as DNA origami are being considered for applications in molecular biology and nanomedicine. However, many DNA structures need a higher ionic strength than that of common cell culture buffers or bodily fluids to maintain their integrity and can be degraded quickly by nucleases. To overcome these deficiencies, we coated several different DNA origami structures with a cationic poly(ethylene glycol)-polylysine block copolymer, which electrostatically covered the DNA nanostructures to form DNA origami polyplex micelles (DOPMs)...
March 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28289761/a-new-biochromatography-model-based-on-dna-origami-assembled-ppar%C3%AE-construction-and-evaluation
#11
Jie Zhou, Lingchang Meng, Chong Sun, Shanshan Chen, Fang Sun, Pei Luo, Yongxing Zhao
As drug targets, receptors have potential to screen drugs. Silica is an attractive support to immobilize receptors; however, the lack of biocompatibility makes it easier for receptors to lose bioactivity, which remains an obstacle to its widespread use. With the advantage of biocompatibility, DNA origami can be used as a biological carrier to improve the biocompatibility of silica and assemble receptors. In this study, a new biochromatography model based on DNA origami was constructed. A large quantity of M13ssDNA was used as a scaffold, leading to significant costs, so M13ssDNA was self-produced from the bacteriophage particles...
March 13, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28287117/barcode-extension-for-analysis-and-reconstruction-of-structures
#12
Cameron Myhrvold, Michael Baym, Nikita Hanikel, Luvena L Ong, Jonathan S Gootenberg, Peng Yin
Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure...
March 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28256790/universal-super-resolution-multiplexing-by-dna-exchange
#13
Florian Schueder, Maximilian T Strauss, David Hoerl, Joerg Schnitzbauer, Thomas Schlichthaerle, Sebastian Strauss, Peng Yin, Hartmann Harz, Heinrich Leonhardt, Ralf Jungmann
Super-resolution microscopy allows optical imaging below the classical diffraction limit of light with currently up to 20× higher spatial resolution. However, the detection of multiple targets (multiplexing) is still hard to implement and time-consuming to conduct. Here, we report a straightforward sequential multiplexing approach based on the fast exchange of DNA probes which enables efficient and rapid multiplexed target detection with common super-resolution techniques such as (d)STORM, STED, and SIM. We assay our approach using DNA origami nanostructures to quantitatively assess labeling, imaging, and washing efficiency...
March 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28249387/-dna-origami-traffic-lights-with-a-split-aptamer-sensor-for-a-bicolor-fluorescence-readout
#14
Heidi-Kristin Walter, Jens Bauer, Jeannine Steinmeyer, Akinori Kuzuya, Christof M Niemeyer, Hans-Achim Wagenknecht
A split aptamer for adenosine triphosphate (ATP) was embedded as a recognition unit into two levers of a nanomechanical DNA origami construct by extension and modification of selected staple strands. An additional optical module in the stem of the split aptamer comprised two different cyanine-styryl dyes that underwent an energy transfer from green (donor) to red (acceptor) emission if two ATP molecules were bound as target molecule to the recognition module and thereby brought the dyes in close proximity. As a result, the ATP as a target triggered the DNA origami shape transition and yielded a fluorescence color change from green to red as readout...
March 8, 2017: Nano Letters
https://www.readbyqxmd.com/read/28241201/automated-quantification-of-the-impact-of-defects-on-the-mechanical-behavior-of-deoxyribonucleic-acid-origami-nanoplates
#15
Bowen Liang, Anand Nagarajan, Michael W Hudoba, Ricardo Alvarez, Carlos E Castro, Soheil Soghrati
Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate...
April 1, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/28221680/single-stranded-dna-production-for-scaffolded-dna-origami
#16
(no author information available yet)
No abstract text is available yet for this article.
April 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28218431/spiral-patterning-of-au-nanoparticles-on-au-nanorod-surface-to-form-chiral-aunr-aunp-helical-superstructures-templated-by-dna-origami
#17
Chenqi Shen, Xiang Lan, Chenggan Zhu, Wei Zhang, Leyu Wang, Qiangbin Wang
Plasmonic motifs with precise surface recognition sites are crucial for assembling defined nanostructures with novel functionalities and properties. In this work, a unique and effective strategy is successfully developed to pattern DNA recognition sites in a helical arrangement around a gold nanorod (AuNR), and a new set of heterogeneous AuNR@AuNP plasmonic helices is fabricated by attaching complementary-DNA-modified gold nanoparticles (AuNPs) to the predesigned sites on the AuNR surface. AuNR is first assembled to one side of a bifacial rectangular DNA origami, where eight groups of capture strands are selectively patterned on the other side...
February 20, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28205515/tailored-protein-encapsulation-into-a-dna-host-using-geometrically-organized-supramolecular-interactions
#18
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
https://www.readbyqxmd.com/read/28196307/molecule-counts-in-localization-microscopy-with-organic-fluorophores
#19
Christos Karathanasis, Franziska Fricke, Gerhard Hummer, Mike Heilemann
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 extract 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
https://www.readbyqxmd.com/read/28168148/protein-functionalized-dna-nanostructures-as-tools-to-control-transcription-in-zebrafish-embryos
#20
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
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