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Dna origami

Zhugen Yang, Gaolian Xu, Julien Reboud, Syed Atif Ali, Gurpreet Kaur, John McGiven, Nongthombam Boby, Praveen Gupta, Pallab Chaudhuri, Jonathan Mark Cooper
The health and well-being of cattle is a significant concern for global agricultural output. In dairy production within low and middle income countries (LMICs), there is a significant biosensing challenge in detecting sexually transmitted infection (STI) pathogens during animal husbandry, due in part to difficulties associated with the limited infrastructure for veterinary medicine. Here we demonstrate low-cost, multiplexed and sample-to-answer paper-origami tests for the detection of three bovine infectious reproductive diseases in semen samples, collected at a test site in rural India...
January 11, 2018: ACS Sensors
Qianqian Shi, Dashen Dong, Kae Jye Si, Debabrata Sikdar, Lim Wei Yap, Malin Premaratne, Wenlong Cheng
Self-assembly of nanoparticles represents a simple yet efficient route to synthesize designer materials with unusual properties. However, the previous assembled structures whether by surfactants, polymer, or DNA ligands are "static" or "frozen" building block structures. Here, we report the growth of transformable self-assembled nanosheets which could enable reversible switching between two types of nanosheets and even evolving into diverse third generation nanosheet structures without losing pristine periodicity...
January 5, 2018: ACS Nano
Ke Liu, Dun Pan, Yanqin Wen, Honglu Zhang, Jie Chao, Lihua Wang, Shiping Song, Chunhai Fan, Yongyong Shi
The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established...
December 28, 2017: Small
Koen Schakenraad, Andreas S Biebricher, Maarten Sebregts, Brian Ten Bensel, Erwin J G Peterman, Gijs J L Wuite, Iddo Heller, Cornelis Storm, Paul van der Schoot
The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA...
December 19, 2017: Nature Communications
Dongran Han, Xiaodong Qi, Cameron Myhrvold, Bei Wang, Mingjie Dai, Shuoxing Jiang, Maxwell Bates, Yan Liu, Byoungkwon An, Fei Zhang, Hao Yan, Peng Yin
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure...
December 15, 2017: Science
Florian Schueder, Juanita Lara-Gutiérrez, Brian J Beliveau, Sinem K Saka, Hiroshi M Sasaki, Johannes B Woehrstein, Maximilian T Strauss, Heinrich Grabmayr, Peng Yin, Ralf Jungmann
Single-molecule localization microscopy (SMLM) can visualize biological targets on the nanoscale, but complex hardware is required to perform SMLM in thick samples. Here, we combine 3D DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) with spinning disk confocal (SDC) hardware to overcome this limitation. We assay our achievable resolution with two- and three-dimensional DNA origami structures and demonstrate the general applicability by imaging a large variety of cellular targets including proteins, DNA and RNA deep in cells...
December 12, 2017: Nature Communications
Chanseok Lee, Jae Young Lee, Do-Nyun Kim
Scaffolded DNA origami enables the bottom-up fabrication of diverse DNA nanostructures by designing hundreds of staple strands, comprised of complementary sequences to the specific binding locations of a scaffold strand. Despite its exceptionally high design flexibility, poor reusability of staples has been one of the major hurdles to fabricate assorted DNA constructs in an effective way. Here we provide a rational module-based design approach to create distinct bent shapes with controllable geometries and flexibilities from a single, reference set of staples...
December 12, 2017: Nature Communications
Luvena L Ong, Nikita Hanikel, Omar K Yaghi, Casey Grun, Maximilian T Strauss, Patrick Bron, Josephine Lai-Kee-Him, Florian Schueder, Bei Wang, Pengfei Wang, Jocelyn Y Kishi, Cameron Myhrvold, Allen Zhu, Ralf Jungmann, Gaetan Bellot, Yonggang Ke, Peng Yin
Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands...
December 6, 2017: Nature
Klaus F Wagenbauer, Christian Sigl, Hendrik Dietz
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging...
December 6, 2017: Nature
Grigory Tikhomirov, Philip Petersen, Lulu Qian
Self-assembled DNA nanostructures enable nanometre-precise patterning that can be used to create programmable molecular machines and arrays of functional materials. DNA origami is particularly versatile in this context because each DNA strand in the origami nanostructure occupies a unique position and can serve as a uniquely addressable pixel. However, the scale of such structures has been limited to about 0.05 square micrometres, hindering applications that demand a larger layout and integration with more conventional patterning methods...
December 6, 2017: Nature
Florian Praetorius, Benjamin Kick, Karl L Behler, Maximilian N Honemann, Dirk Weuster-Botz, Hendrik Dietz
DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used...
December 6, 2017: Nature
Alex Stopar, Lucia Coral, Stefano Di Giacomo, Abimbola F Adedeji, Matteo Castronovo
Controlling DNA nanostructure interaction with protein is essential in developing nanodevices with programmable function, reactivity, and stability for biological and medical applications. Here, we show that the sequence-specific action of restriction endonucleases towards sharp triangular or rectangular DNA origami exhibits a novel, binary 'on/off' behaviour, as canonical recognition sites are either essentially fully reactive, or strongly resistant to enzymatic cutting. Moreover, introduction of structural defects in the sharp triangle can activate an otherwise unreactive site, with a site-to-defect distance of ∼50 nm...
December 4, 2017: Nucleic Acids Research
Yu Tokura, Sean Harvey, Chaojian Chen, Yuzhou Wu, David Yuen Wah Ng, Tanja Weil
A versatile, bottom-up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage-mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase-mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution...
December 6, 2017: Angewandte Chemie
Elisha Krieg, William M Shih
Scalable methods currently are lacking for isolation of long ssDNA, an important material for numerous biotechnological applications. Conventional biomolecule purification strategies achieve target capture using solid supports, which are limited in scale and susceptible to contamination due to nonspecific adsorption and desorption on the substrate surface. We herein disclose Selective Nascent Polymer Catch and Release (SNAPCAR), a method that utilizes the reactivity of growing poly(acrylamide-co-acrylate) chains to capture acrylamide-labeled molecules in free solution...
December 5, 2017: Angewandte Chemie
Xin Luo, Pongphak Chidchob, Janane F Rahbani, Hanadi F Sleiman
Gold nanoparticles (AuNPs) endowed with anisotropic DNA valency are an important class of materials, as they can assemble into complex structures with a minimal number of DNA strands. However, methods to encode 3D DNA strand patterns on AuNPs with a controlled number of unique DNA strands in a predesigned spatial arrangement remain elusive. In this work, a simple one-step method to yield such DNA-decorated AuNPs is demonstrated, through encapsulating AuNPs into DNA minimal nanocages. The AuNP@DNA cage encapsulation complex inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability...
December 4, 2017: Small
Andrew James Lee, Masayuki Endo, Jamie Kayne Hobbs, Christoph Walti
Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous Recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging...
December 4, 2017: ACS Nano
Eric Beamish, Vincent Tabard-Cossa, Michel Godin
The identification of molecular tags along nucleic acid sequences has many potential applications in bionanotechnology, disease biomarker detection and DNA sequencing. An attractive approach to this end is the use of solid-state nanopores, which can electrically detect molecular substructure and can be integrated into portable lab-on-a-chip sensors. We present here a DNA origami-based approach of molecular assembly in which solid-state nanopores are capable of differentiating 165 bp scaffolds containing zero, one and two dsDNA protrusions...
November 28, 2017: ACS Sensors
Yi Chen, Ping Wang, Yang Liu, Ting Liu, Yan Xu, Shanshan Zhu, Jun Zhu, Kai Ye, Guang Huang, Dannong He
We synthesized triangular and rectangular DNA origami nanostructures and investigated the stability and recovery of it under low cation concentration. Our results demonstrate that the origami nanostructures degrade when incubated in low cation concentration, and recover themselves while stay in the concentration for less than 10 minutes. However, extending the incubation time leads to an irreversible degradation. Our results show a possibility of application of DNA origami nanostructures such as a sensor for cation concentration response or isothermal amplification, etc...
November 28, 2017: Nanotechnology
Hyojeong Kim, Kristin Arbutina, Anqin Xu, Haitao Liu
We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al2O3. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O3 oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films...
2017: Beilstein Journal of Nanotechnology
Yuhe R Yang, Jinglin Fu, Shaun Wootten, Xiaodong Qi, Minghui Liu, Hao Yan, Yan Liu
In living cells, compartmented or membrane-associated enzymes are often assembled into large networks for cooperatively catalyzing cascade reaction pathways essential for the cellular metabolism. Here, we report the assembly of an artificial 2D enzyme network of two cascade enzymes, glucose-6-phosphate dehydrogenase (G6PDH) and lactate dehydrogenase (LDH) on a wireframe DNA origami template. Swinging arms were used to facilitate the transport of redox intermediate of NAD+/NADH between enzyme pairs on the array...
November 27, 2017: Chembiochem: a European Journal of Chemical Biology
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