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dna nanostructure

Lindong Weng, Mehmet Toner
Deep eutectic solvents (DESs) have emerged as a set of intrinsically "designer solvents" for many bio-applications such as DNA nanotechnology and biocatalysis. However, the high viscosity of DESs tends to prevent bioactive components from being incorporated into the solvent. Although dilution with water may effectively reduce the viscosity of DES, the effect of water on its cooperative hydrogen-bonding network has not been evaluated systematically. This study conducted a series of molecular dynamics simulations on the DES made of choline chloride and glycerol at different hydration levels...
July 19, 2018: Physical Chemistry Chemical Physics: PCCP
Betul Oruc, Suleyman Celik, Serap Hayat Soytas, Hayriye Unal
Utilization of a self-assembled two-dimensional DNA nanostructure to arrange single-walled carbon nanotubes (SWNTs) into predetermined structures at controllable angles is presented. A specially designed DNA three-way junction (3WJ) composed of three double-stranded DNA arms containing single-stranded overhang sequences was prepared by annealing of partially complementary ssDNA sequences and ultrasonicated with SWNTs, resulting in DNA-3WJ/SWNT hybrid nanostructures. Utilization of DNA-3WJ not only allowed the precise dispersion of SWNTs but also acted as a rigid template for the self-assembly of SWNTs into three-armed junctions at an angle of approximately 120° to each other as visualized by scanning electron microscopy and atomic force microscopy...
April 30, 2018: ACS Omega
Shern Ren Tee, Zhisong Wang
A purely DNA nanomachine must support internal stresses across short DNA segments with finite rigidity, producing effects that can be qualitatively very different from experimental observations of isolated DNA in fixed-force ensembles. In this article, computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-stranded segments and how well this stress can discriminate between unzipping or shearing geometries. This discrimination is found to be maximized at an optimal length but deteriorates as the driving duplex is either lengthened or shortened...
January 31, 2018: ACS Omega
María Martínez-Negro, Andrés Guerrero-Martínez, Luis García-Río, Òscar Domènech, Emilio Aicart, Conchita Tros de Ilarduya, Elena Junquera
A multidisciplinary strategy, including both biochemical and biophysical studies, was proposed here to evaluate the potential of lipid nanoaggregates consisting of a mixture of a gemini-bolaamphiphilic lipid (C6 C22 C6 ) and the well-known helper lipid 1,2-dioleoyl- sn -glycero-3-phosphatidylethanolamine (DOPE) to transfect plasmid DNA into living cells in an efficient and safe way. For that purpose, several experimental techniques were employed, such as zeta potential (phase analysis light scattering methodology), agarose gel electrophoresis (pDNA compaction and pDNA protection assays), small-angle X-ray scattering, cryo-transmission electron microscopy, atomic force microscopy, fluorescence-assisted cell sorting, luminometry, and cytotoxicity assays...
January 31, 2018: ACS Omega
Masayuki Endo, Hiroshi Sugiyama
DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements...
July 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Ruizi Peng, Xiaofang Zheng, Yifan Lyu, Liujun Xu, Xiao-Bing Zhang, Guoliang Ke, Qiaoling Liu, Changjun You, Shuangyan Huan, Weihong Tan
Among the vast number of recognition molecules, DNA ap-tamers generated from cell-SELEX exhibit unique properties for identifying cell membrane biomarkers, in particular pro-tein receptors on cancer cells. To integrate all recognition and computing modules within a single structure, a three-dimensional (3D) DNA-based logic gate nanomachine was constructed to target overexpressed cancer cell biomarkers with bispecific recognition. Thus, when the Boolean opera-tor "AND" returns a true value, it is followed by an "ON" signal when the specific cell type is presented...
July 18, 2018: Journal of the American Chemical Society
Libo Zhu, Ying Xu, Irshad Ali, Liping Liu, Hongwen Wu, Zuhong Lu, Quanjun Liu
The detection and investigation of biomolecules at a single molecule level is important for improving diagnosis in biomedicine. Solid-state nanopores are a unique tool that have the potential to accomplish this task, because they are label-free, and require only low sample consumption. However, the event-readouts of current small polymer molecules are still limited due to its relatively large size and low signal-to-noise ratios. Here, we present a rapid sensing approach for the detection of GR-5 DNAzyme cleaving specific substrate reactions using relatively larger size silicon nitride nanopores by introducing a type of nucleic acid nanostructure (DNA tetrahedron) as a carrier...
July 17, 2018: ACS Applied Materials & Interfaces
Huihui Wang, Jiao Zheng, Yudie Sun, Tao Li
Here we report smart molecular logic circuits built on a well-designed H-shaped DNA nanostructure that can recognize cell-simulated bioenvironments and modulate the operations of a DNA nanosensor. By assembling a wild-type ATP aptamer and a parallel G-quadruplex into the H-shaped DNA scaffold, two intrinsic cellular components, ATP and K+ , are utilized to activate the logic circuits, enabling fluorescent detection of the target DNA via toehold-mediated strand displacement. In this way, two logic circuits consisting of cascaded "AND-AND" and "OR-AND" gates are achieved, which are responsive to the ATP and/or K+ concentration change outside and inside cells, and therefore control whether or not the downstream DNA sensor works...
July 6, 2018: Biosensors & Bioelectronics
Xiaoguo Liu, Fei Zhang, Xinxin Jing, Muchen Pan, Pi Liu, Wei Li, Bowen Zhu, Jiang Li, Hong Chen, Lihua Wang, Jianping Lin, Yan Liu, Dongyuan Zhao, Hao Yan, Chunhai Fan
Genetically encoded protein scaffolds often serve as templates for the mineralization of biocomposite materials with complex yet highly controlled structural features that span from nanometres to the macroscopic scale1-4 . Methods developed to mimic these fabrication capabilities can produce synthetic materials with well defined micro- and macro-sized features, but extending control to the nanoscale remains challenging5,6 . DNA nanotechnology can deliver a wide range of customized nanoscale two- and three-dimensional assemblies with controlled sizes and shapes7-11 ...
July 16, 2018: Nature
Ali Ghanim Al-Rubaye, Alexei Nabok, Gaelle Catanante, Jean-Louis Marty, Eszter Takács, András Székács
This work focuses on the development of the novel label-free optical apta-sensors for detection of mycotoxins. A highly sensitive analytical method of total internal reflection ellipsometry (TIRE) combined with Localized Surface Plasmon Resonance (LSPR) phenomenon in nano-structured gold films was exploited here for the first time for detection of aflatoxin B1 and M1 in direct assay with specific aptamers immobilized on the surface of gold. The achieved detection of low molecular weight molecules, such as aflatoxin B1 and M1, in a wide range of concentrations from 100 ng/mL down to 0...
July 16, 2018: Toxins
Pu Zhang, Jie Jiang, Ruo Yuan, Ying Zhuo, Yaqin Chai
Herein, by directly using Watson-Crick base pairing, a highly ordered and field-free 3D DNA nanostructure is self-assembled by azobenzene (azo)-functionalized DNA nippers in few minutes, which was applied as three-dimensional (3D) DNA nanomachine with an improved movement efficiency compared to traditional Au-based 3D nanomachines due to the organized and high local concentration of nippers on homogeneous DNA nanostructure. Once microRNA (miRNA) interacts with the 3D nanomachine, the nippers "open" to hybridize with the miRNA...
July 16, 2018: Journal of the American Chemical Society
Simon Chi-Chin Shiu, Andrew Brian Kinghorn, Yusuke Sakai, Yee-Wai Cheung, Jonathan Gardiner Heddle, Julian Alexander Tanner
DNA aptamers are ideal tools to enable modular control of DNA nanostructure dynamics. For molecular recognition they have a particular advantage compared to antibodies, namely they can be integrated into DNA nanostructures in a bespoke manner by base-pairing or nucleotide extension without any complex bioconjugation strategy. Such simplicity will be critical when considering advanced therapeutic and diagnostic applications of DNA nanostructures. However, optimizing DNA aptamers for functional control of DNA nanostructure dynamics can be challenging...
July 14, 2018: Chembiochem: a European Journal of Chemical Biology
Elyas Hosseinzadeh, Hadi Ravan, Abbas Mohammadi, Rahim Mohammad-Rezaei, Akram Norouzi, Hossein Hosseinzadeh
With the great advances in DNA nanotechnology, scientists have shown interest in developing dynamic nanostructures for theranostic applications, analyte sensing and cargo delivery. Here, we present a specific enzyme-free ultrasensitive platform based on a multilayer coupled signal amplification strategy to quantify miR-21 molecule. The biosensor was integrated based on three signal amplification gadgets, namely a translator-mediated catalytic hairpin assembly (CHA), a multilayer DNA concatemer on the surface of gold decorated magnetic nanoparticle (GMNP), and a DNAzyme-mediated catalytic signal amplification...
June 28, 2018: Biosensors & Bioelectronics
Hongjie Qi, Shuzhen Yue, Sai Bi, Caifeng Ding, Weiling Song
We demonstrate a strategy for pH-programmable self-assembly of DNA nanostructures by taking advantage of the pH dependence of reverse Hoogsteen interactions for a triplex-helix molecular switch. This strategy is successfully applied to the construction of molecular logic gates and imaging of extracellular pH.
July 13, 2018: Chemical Communications: Chem Comm
Chenggan Zhu, Meng Wang, Jinyi Dong, Chao Zhou, Qiangbin Wang
Arraying noble metal nanoparticles at the nanoscale features an important way towards plasmonic devices with novel optical properties such as plasmonic chiral metamolecules, optical waveguides, etc. Along with top-down methods of fabricating plasmonic nanostructures, solution-based self-assembly provides an alternative approach. There are mainly two routes of organizing metal nanoparticles via self-assembly. One is directly linking nanoparticles through some linker molecules, while the other one is decorating nanoparticles on a pre-formed template...
July 12, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Simon Chi-Chin Shiu, Lewis A Fraser, Yifan Ding, Julian A Tanner
DNA aptamers are important tools for molecular recognition, particularly for a new generation of tools for biomedicine based on nucleic acid nanostructures. Here, we investigated the relative abilities of different shapes and sizes of DNA polyhedra to display an aptamer which binds to the malaria biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH). The aptamer was shown to perform an Aptamer-Tethered Enzyme Capture (APTEC) assay with the hypothesis that the display of the aptamer above the surface through the use of a polyhedron may lead to better sensitivity than use of the aptamer alone...
July 11, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Tong Lin, Jun Yan, Luvena L Ong, Joanna Robaszewski, Hoang D Lu, Yongli Mi, Peng Yin, Bryan Wei
Because of its attractive cost and yield, hierarchical assembly, in which constituent structures of lower hierarchy share a majority of components, is an appealing approach to scale up DNA self-assembly. A few strategies have already been investigated to combine preformed DNA nanostructures. In this study, we present a new hierarchical assembly method based on four-way toehold-mediated strand displacement to facilitate the combination of preformed DNA structural units. Employing such a method, we have constructed a series of higher-order structures composed of 5, 7, 9, 11, 13, and 15 preformed units respectively...
July 10, 2018: Nano Letters
Xiaoxing Chen, Qian Wang, Jin Peng, Qipeng Long, Hanyang Yu, Zhe Li
As a milestone in DNA self-assembly, DNA origami has demonstrated powerful applications in many fields. However, the scarce availability of long single-stranded DNA (ssDNA) limits the size and sequences of DNA origami nanostructures, which in turn impedes the further development. In this study, we present a robust strategy to produce long circular ssDNA scaffold strands with custom-tailored lengths and sequences. These ssDNA products were then used as scaffolds for constructing various DNA origami nanostructures...
July 10, 2018: ACS Applied Materials & Interfaces
Danny Bousmail, Pongphak Chidchob, Hanadi F Sleiman
Supramolecular one-dimensional (1D) architectures are of high interest in drug delivery and templation of complex linear arrays due to their high aspect ratio and rigidity. A particular desire is the access of 1D nanostructures with high functionality and bio-relevance, which opens the door to a wide variety of their applications in materials science and nanomedicine. Here, we report the discovery that the site-specific introduction of a cyanine (Cy3) dye unit in sequence-defined DNA amphiphiles causes a complete shift of the overall structure from spheres to 1D DNA nanofibers in aqueous media...
July 9, 2018: Journal of the American Chemical Society
Li Zhou, Yu Liu, Hui Shi, Xiaohai Yang, Jin Huang, Songyang Liu, Qiaoshu Chen, Jianbo Liu, Kemin Wang
Spatial organization of multienzyme at specific positions for controlled reaction cascade has attracted wide attentions. Here, we report the construction of a biomimetic enzyme cascade organizing on DNA triangle prism (TP) nanostructures, which enabled efficient catalytical production of nitric oxide (NO) on a single microbead. Two enzymes, glucose oxidase (GOx) and horseradish peroxidase (HRP), were assembled at adjacent locations on DNA TP nanostructure by using DNA-binding protein adaptors with small interenzyme distances...
July 9, 2018: Chembiochem: a European Journal of Chemical Biology
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