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https://www.readbyqxmd.com/read/29311611/an-adaptive-supramolecular-hydrogel-comprising-self-sorting-double-nanofibre-networks
#1
Hajime Shigemitsu, Takahiro Fujisaku, Wataru Tanaka, Ryou Kubota, Saori Minami, Kenji Urayama, Itaru Hamachi
Novel soft materials should comprise multiple supramolecular nanostructures whose responses (for example, assembly and disassembly) to external stimuli can be controlled independently. Such multicomponent systems are present in living cells and control the formation and break-up of a variety of supramolecular assemblies made of proteins, lipids, DNA and RNA in response to external stimuli; however, artificial counterparts are challenging to make. Here, we present a hybrid hydrogel consisting of a self-sorting double network of nanofibres in which each network responds to an applied external stimulus independent of the other...
January 8, 2018: Nature Nanotechnology
https://www.readbyqxmd.com/read/29310288/self-assembly-of-dna-nanoparticles-through-multiple-catalyzed-hairpin-assembly-for-enzyme-free-nucleic-acid-amplified-detection
#2
Hongfei He, Jianyuan Dai, Yan Meng, Zhijuan Duan, Cuisong Zhou, Baozhan Zheng, Juan Du, Yong Guo, Dan Xiao
It is known that DNA molecules can be used to build a various of complicated geometrical DNA nanostructures with programmable sequence design, and these DNA nanomaterials show a promising application in biotechnology and biomedicine. However, the construction of large-sized three dimensional DNA-based nanomaterials still remains a challenge. In this work, we propose a new strategy that only employs one target DNA to trigger multiple catalyzed hairpin assembly (CHA) reactions and sticky ends self-assembly to prepare hundreds of nanometer-sized DNA nanoparticles...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29302054/controlling-protein-activity-by-dynamic-recruitment-on-a-supramolecular-polymer-platform
#3
Sjors P W Wijnands, Wouter Engelen, René P M Lafleur, E W Meijer, Maarten Merkx
Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins...
January 4, 2018: Nature Communications
https://www.readbyqxmd.com/read/29300456/anti-inflammatory-and-anti-oxidative-effects-of-tetrahedral-dna-nanostructures-via-the-modulation-of-macrophage-responses
#4
Qi Zhang, Shiyu Lin, Sirong Shi, Tao Zhang, Quanquan Ma, Taoran Tian, Tengfei Zhou, Xiaoxiao Cai, Yunfeng Lin
Tetrahedral DNA nanostructures (TDNs) are a new type of nano-materials that have recently attracted attention in the field of biomedicine. However, the practical application of nanomaterials is often limited owing to the host immune response. Here, the response of RAW264.7 macrophages to TDNs was comprehensively evaluated. The results showed that TDNs had no observable cytotoxicity and could induce polarization of RAW264.7 cells to M1 type. TDNs attenuated the expression of NO IL-1β (Interleukin-1β), IL-6 (interleukin-6), and TNF-α (tumor necrosis factor-α) in LPS-induced RAW264...
January 4, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29299920/targeted-imaging-of-brain-tumors-with-a-framework-nucleic-acid-probe
#5
Tian Tian, Jiang Li, Cao Xie, Yanhong Sun, Haozhi Lei, Xinyi Liu, Jiaoyun Xia, Jiye Shi, Lihua Wang, Weiyue Lu, Chunhai Fan
Development of agents for delivering drugs and imaging probes across the blood brain barrier (BBB) remains a major challenge. In this study, we designed a biocompatible framework nucleic acid (FNA)-based imaging probe for brain tumor targeting. We employed a typical type of FNAs, tetrahedral DNA nanostructures (TDNs), as the building block, which were modified with angiopep-2 (ANG), a 19-mer peptide derived from human Kunitz domain of aprotinin. This probe exhibited high binding efficiency with low-density lipoprotein receptor-related protein-1 (LRP-1) of BBB and glioma...
January 4, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29283218/identifying-the-genotypes-of-hepatitis-b-virus-hbv-with-dna-origami-label
#6
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
https://www.readbyqxmd.com/read/29280620/a-novel-electrochemiluminescence-peptide-based-biosensor-with-hetero-nanostructures-as-co-reaction-accelerator-for-the-ultra-sensitive-determination-of-tryptase
#7
Fang-Fang Wu, Ying Zhou, Han Zhang, Ruo Yuan, Ya-Qin Chai
In this work, a luminol-centric biosensor was constructed for the ultrasensitive detection of tryptase (TPS) combining dissolved O2 as the endogenous coreactant and Au-Ag-Pt hetero-nanostructures (AAPHNs) as co-reaction accelerator. Dissolved O2 could rapidly generate superoxide anion radical (O2•-) with the catalysis of AAPHNs to in situ react with luminol anion radical (L•-) to generate excited-state species 3-aminophthalate (AP2-*) for emitting ECL signal, resulting in a remarkable "single on" state...
December 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29276894/a-structure-based-assembly-screen-of-protein-cage-libraries-in-living-cells-experimentally-repacking-a-protein-protein-interface-to-recover-cage-formation-in-an-assembly-frustrated-mutant
#8
Thomas Cornell, Maziar S Ardejani, Jing Fu, Stephanie Newland, Yu Zhang, Brendan P Orner
Cage proteins, which assemble into often highly symmetric hollow nano-scale capsules, have great potential in ap-plications as far reaching as drug delivery, hybrid nanomaterial engineering, and catalysis. In addition, they are promising model systems to understand how cellular nanostructures are constructed through protein-protein interactions, and they are beginning to be used as scaffolds for synthetic biology approaches. Recently, there has been renewed interest in the engineering of protein cages and, in support of these strategies, we have recently described a fluorescence-based assay for protein cage assembly that is specific for certain oligomerization states and symmetry-related protein-protein interfaces...
December 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/29261298/how-to-tune-the-gene-delivery-and-biocompatibility-of-poly-2-4-aminobutyl-2-oxazoline-by-self-and-co-assembly
#9
Meike N Leiske, Fabian H Sobotta, Stephanie Hoeppener, Johannes C Brendel, Anja Traeger, Ulrich S Schubert
Despite their promising potential in gene transfection, the toxicity and limited efficiency of cationic polymers as non-viral vectors are major obstacles for their broader application. The large amount of cationic charges, e.g. in poly(ethylene imine) (PEI) is known to be advantageous in terms of their transfection efficiency, but goes hand-in-hand with a high toxicity. Consequently, an efficient shielding of the charges is required to minimize toxic effects. In this study, we use a simple mixed micelle approach to optimize the required charge density for efficient DNA complex formation and to minimize toxicity by using a biocompatible polymer...
December 20, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29250433/insights-into-origin-and-evolution-of-%C3%AE-proteobacterial-gene-transfer-agents
#10
Migun Shakya, Shannon M Soucy, Olga Zhaxybayeva
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29242318/single-stranded-dna-and-rna-origami
#11
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
https://www.readbyqxmd.com/read/29233997/polymorphic-design-of-dna-origami-structures-through-mechanical-control-of-modular-components
#12
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
https://www.readbyqxmd.com/read/29232197/dna-based-construction-at-the-nanoscale-emerging-trends-and-applications
#13
Lourdu Xavier Paulraj, Arun Richard Chandrasekaran
The field of structural DNA nanotechnology has reached adolescence - starting with the creation of artificial immobile junctions leading to the recent DNA-protein hybrid nanoscale shapes - in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields...
December 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29228337/triplex-forming-oligonucleotides-a-third-strand-for-dna-nanotechnology
#14
Arun Richard Chandrasekaran, David A Rusling
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure...
December 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29226453/silver-i-mediated-base-pairs-in-dna-sequences-containing-7-deazaguanine-cytosine-base-pairs-towards-dna-with-entirely-metallated-watson-crick-base-pairs
#15
José M Méndez-Arriaga, Carmen R Maldonado, José A Dobado, Miguel A Galindo
DNA sequences comprising non-canonical 7-deazaguanine (7CG) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplex I and II containing 7CG and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV-spectroscopy, circular dichroism and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7CG-AgI-C Watson-Crick base pairs that preserve the original B-type conformation...
December 10, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29219968/programmable-self-assembly-of-three-dimensional-nanostructures-from-10-000-unique-components
#16
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
https://www.readbyqxmd.com/read/29219965/fractal-assembly-of-micrometre-scale-dna-origami-arrays-with-arbitrary-patterns
#17
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
https://www.readbyqxmd.com/read/29219963/biotechnological-mass-production-of-dna-origami
#18
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
https://www.readbyqxmd.com/read/29216375/binary-control-of-enzymatic-cleavage-of-dna-origami-by-structural-antideterminants
#19
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
https://www.readbyqxmd.com/read/29214256/thermally-reversible-nanoparticle-gels-with-tuneable-porosity-showing-structural-colour
#20
Z Ruff, P Cloetens, T O'Neill, C P Grey, E Eiser
We present colloidal gels formed from dispersions of PEG- and PEG+DNA-coated silica nanoparticles showing structural colour. The PEG- and PEG+DNA-coated silica colloids are functionalized using exclusively covalent bonds in aqueous conditions. Both sets of colloids self-assemble into thermally-reversible colloidal gels with porosity that can be tuned by changing the colloid volume fraction, although the interaction potentials of the colloids in the two systems are different. Confocal microscopy and image analysis tools are used to characteraize the gels' microstructures...
December 7, 2017: Physical Chemistry Chemical Physics: PCCP
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