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dna nanostructure

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
Resham J Banga, Brian Meckes, Suguna P Narayan, Anthony J Sprangers, SonBinh T Nguyen, Chad A Mirkin
A one-pot synthesis of micellar spherical nucleic acid (SNA) nanostructures using Pluronic F127 as a thermoresponsive template is reported. These novel constructs are synthesized in a chemically straightforward process that involves intercalation of the lipid tails of DNA amphiphiles (CpG motifs for TLR-9 stimulation) into the hydrophobic regions of Pluronic F127 micelles followed by chemical cross-linking and subsequent removal of non-crosslinked structures. The dense nucleic acid shell of the resulting cross-linked micellar SNA enhances their stability in physiological media and facilitates their rapid cellular internalization making them effective TLR-9 immunomodulatory agents...
February 16, 2017: Journal of the American Chemical Society
Xiangmeng Qu, Hongbo Zhang, Hong Chen, Ali Aldalbahi, Li Li, Yang Tian, David A Weitz, Hao Pei
One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing contents of droplets with nano or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull-down. The convective flux enables complete reaction in less than 5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of stationary case)...
February 16, 2017: Analytical Chemistry
Yangyang Yang, Ryu Tashiro, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo
Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule, was placed on the top of a rectangular DNA tile. The photoresponsive oligonucleotides modified with azobenzenes were employed as switching motifs to release/trap the rotor at specific angular position on DNA tile by switching photoirradiations between ultraviolet and visible light...
February 15, 2017: Chemistry: a European Journal
Jing Su, Dongfang Wang, Lena Nörbel, Jianlei Shen, Zhihan Zhao, Yanzhi Dou, Tianhuan Peng, Jiye Shi, Sanjay Mathur, Chunhai Fan, Shiping Song
Uniform silver-containing metal nanostructures with strong and stable surface-enhanced Raman scattering (SERS) signals hold great promise for developing ultrasensitive probes for biodetection. Nevertheless, the direct synthesis of such ready-to-use nanoprobes remains extremely challenging. Herein we report a DNA-mediated gold-silver nanomushroom with interior nanogaps directly synthesized and used for multiplex and simultaneous SERS detection of various DNA and RNA targets. The DNA involved in the nanostructures can act as not only gap DNA (mediated DNA) but also probe DNA (hybridized DNA), and DNA's involvement enables the nanostructures to have the inherent ability to recognize DNA and RNA targets...
February 9, 2017: Analytical Chemistry
Chikara Dohno, Shingo Makishi, Kazuhiko Nakatani, Sonia Contera
Future lipid membrane-associated DNA nanostructures are expected to find applications ranging from synthetic biology to nanomedicine. Here we have designed and synthesized DNA tiles and modified them with amphiphilic covalent moieties. dod-DEG groups, which consist of a hydrophilic diethylene glycol (DEG) and a hydrophobic dodecyl group, are introduced at the phosphate backbone to create amphiphilic DNA strands which are subsequently introduced into one face of the DNA tiles. In this way the tile becomes able to stably bind to lipid membranes by insertion of the hydrophobic groups inside the bilayer core...
February 10, 2017: Nanoscale
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
Yingning Gao, Samson Or, Aaron Toop, Ian Wheeldon
Understanding the molecular interactions between small molecules and double-stranded DNA has important implications on the design and development of DNA and DNA-protein nanomaterials. Such materials can be assembled into a vast array of 1-, 2-, and 3D structures that contain a range of chemical and physical features where small molecules can bind via intercalation, groove binding, and electrostatics. In this work, we use a series of simulation-guided binding assays and spectroscopy techniques to investigate the binding of selected organophosphtates, methyl parathion, paraoxon, their common enzyme hydrolysis product p-nitrophenol, and double-stranded DNA fragments and DNA DX tiles, a basic building block of DNA-based materials...
February 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Arivazhagan Rajendran, Eiji Nakata, Shun Nakano, Takashi Morii
Cellular metabolism involves complex sequences of organized enzymatic reactions, known as metabolic pathways, that convert substrates into readily usable materials. Nature organizes these enzymatic complexes in a well-defined manner so that the cascade reactions are more rapid and efficient than it would be if the enzymes were randomly distributed in cytosol - the liquid found inside cells. Development of artificial enzyme cascades that resembles the nature's concept of sequentially assembled enzymes is of current interest due to its applications from diagnostics to the production of high-value chemicals...
February 2, 2017: Chembiochem: a European Journal of Chemical Biology
Yonghua Ma, Yan Lu, Guiquan Guan, Jianxun Luo, Qingli Niu, Junlong Liu, Hong Yin, Guangyuan Liu
In this study, we described a novel and effective flower-like ZnO nanostructure assisted Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) method to detect Japanese Encephalitis Virus (JEV). The effects of different concentrations of ZnO nanoflower on the RT-LAMP reaction were investigated. With the increase of concentration of ZnO nanoflower, RT-LAMP reaction obtained optimization, until the concentration exceeded 1.5nM, RT-LAMP reaction was inhibited. Made 1nM as optimum concentration of ZnO nanoflower, we found that optimum RT-LAMP reaction temperature and time were 60°C and 30min, respectively...
January 27, 2017: Virus Research
Pu Zhang, Zhaoyang Li, Haijun Wang, Ying Zhuo, Ruo Yuan, Yaqin Chai
The construction of DNA nanomachines holds great significance in the development of DNA nanostructures; however, the real application of nanomachines is still in its early stage. Moreover, one-step regenerated sensing platforms for the detection of biomarkers in the current research remain a practical challenge. Herein, a novel electrochemiluminescence resonance energy transfer (ERET) strategy between Alexa Flour 488 (AF 488), which is a type of small molecule dye, as the donor and CdSe@ZnS quantum dots (QDs) as the acceptor, which easily enter the cells, has been reported and was applied for the construction of a DNA nanomachine-based regenerated biosensor for the ultra-high sensitive determination of cancer cells without any enzyme...
January 30, 2017: Nanoscale
Giselle S Santos, Cesar A S Andrade, Igor S Bruscky, Leandro B Wanderley, Fabio L Melo, Maria D L Oliveira
Schistosomiasis is a neglected disease closely related to the low levels of social development and a serious public health problem. In this work, we performed an electrochemical detection of Schistosoma mansoni DNA with a self-assembled monolayer of mercaptobenzoic acid (MBA) immobilizing nanostructures composed of gold nanoparticles (AuNPs) and magnetite nanoparticles (Fe3O4_NPs). Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were used to monitor the hybridization process. MBA-Fe3O4_NPs-AuNPs-DNAprobe system reveals an effective electrochemical response indicating the surface modification...
January 20, 2017: Journal of Pharmaceutical and Biomedical Analysis
Aby Konampurath George, Harpreet Singh
With the recent developments in DNA nanotechnology, DNA has been used as the basic building block for the design of nanostructures, autonomous molecular motors, various devices, and circuits. DNA is considered as a possible candidate for replacing silicon for designing digital circuits in a near future, especially in implantable medical devices, because of its parallelism, computational powers, small size, light weight, and compatibility with bio-signals. The research in DNA digital design is in early stages of development, and electrical and computer engineers are not much attracted towards this field...
December 2, 2016: IEEE Transactions on Nanobioscience
Xiaoru Shao, Shiyu Lin, Qiang Peng, Sirong Shi, Xueqin Wei, Tao Zhang, Yunfeng Lin
Utilizing biomaterials to regulate the phenotype and proliferation of chondrocytes is a promising approach for effective cartilage tissue regeneration. Recently, a significant amount of effort has been invested into directing chondrocytes toward a desired location and function by utilizing biomaterials to control the dedifferentiation and phenotypic loss of chondrocytes during in vitro monolayer culture. Here, the transmission signals resulting from tetrahedral DNA nanostructures (TDNs) in the regulation of chondrocyte phenotype and proliferation are exploited...
January 23, 2017: Small
Sybilla Louise Corbett, Rajan Sharma, Alexander Giles Davies, Christoph Wälti
The use of DNA as a structural material for nanometre-scale construction has grown extensively over the last decades. The development of more advanced DNA-based materials would benefit from a modular approach enabling the direct assembly of additional elements onto nanostructures after fabrication. RecA-based nucleoprotein filaments encapsulating short ssDNA have been demonstrated as a tool for highly efficient and fully programmable post-hoc patterning of duplex DNA scaffold. However, the underlying assembly process is not fully understood, in particular when patterning complex DNA topologies...
January 23, 2017: Scientific Reports
Diana Zhang, Paul J Paukstelis
DNA is now one of the most widely used molecules for programmed self-assembly of discrete nanostructures. One of the long-standing goals of the DNA nanotechnology field has been the assembly of periodic, macroscopic 3D DNA crystals for controlled positioning of guest molecules to be used in a variety of applications. With continuing successes in assembling DNA crystals, there is an enhanced need to tailor macroscopic crystal properties-including morphology-to enable their integration into more complex systems...
January 27, 2017: Journal of the American Chemical Society
Oscar Mendoza, Said Houmadi, Jean-Pierre Aimé, Juan Elezgaray
Logic circuits based on DNA strand displacement reaction are the basic building blocks of future nanorobotic systems. The circuits tethered to DNA origami platforms present several advantages over solution-phase versions where couplings are always diffusion-limited. Here we consider a possible implementation of one of the basic operations needed in the design of these circuits, namely, signal replication. We show that with an appropriate preparation of the initial state, signal replication performs in a reproducible way...
January 14, 2017: Journal of Chemical Physics
Phil De Luna, Sahar S Mahshid, Jagotamoy Das, Binquan Luan, Edward H Sargent, Shana O Kelley, Ruhong Zhou
High-curvature electrodes facilitate rapid and sensitive detection of a broad class of molecular analytes. These sensors have reached detection limits not attained using bulk macroscale materials. It has been proposed that immobilized DNA probes are displayed at a high deflection angle on the sensor surface, which allows greater accessibility and more efficient hybridization. Here we report the first use of all-atom molecular dynamics simulations coupled with electrochemical experiments to explore the dynamics of single-stranded DNA immobilized on high-curvature versus flat surfaces...
January 13, 2017: Nano Letters
Bibek Uprety, Tyler Westover, Michael Stoddard, Kamron Brinkerhoff, John Jensen, Robert C Davis, Adam T Woolley, John N Harb
An improved method for the metallization of DNA origami is examined in this work. DNA origami, a simple and robust method for creating a wide variety of nanostructured shapes and patterns, provides an enabling template for bottom-up fabrication of next-generation nanodevices. Selective metallization of these DNA templates is needed to make nanoelectronic devices. Here, we demonstrate a metallization process that uses gold nanorod seeds followed by anisotropic plating to provide improved morphology and greater control of the final metallized width of the structure...
January 11, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
J M Majikes, J A Nash, T H LaBean
Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2...
January 11, 2017: Nanoscale
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