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DNA nanotechnology

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https://www.readbyqxmd.com/read/28335417/dna-sequencing-sensors-an-overview
#1
REVIEW
Jose Antonio Garrido-Cardenas, Federico Garcia-Maroto, Jose Antonio Alvarez-Bermejo, Francisco Manzano-Agugliaro
The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger...
March 14, 2017: Sensors
https://www.readbyqxmd.com/read/28334880/dna-nanostructures-constructed-with-multi-stranded-motifs
#2
Donglei Yang, Zhenyu Tan, Yongli Mi, Bryan Wei
Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28327725/a-four-helix-bundle-dna-nanostructure-with-binding-pockets-for-pyrimidine-nucleotides
#3
Rainer Joachim Schwarz, Clemens Richert
Designed DNA nanostructures of impressive size have been described, but designed structures of the size of protein enzymes that bind organic ligands with high specificity are rare. Here we report a four-helix motif consisting of three synthetic strands with 65 base pairs and 165 nucleotides in total that folds well. Furthermore, we show that in the interior of this small folded DNA nanostructure, cavities can be set up that bind pyrimidine nucleotides with micromolar affinity. Base-specific binding for both thymidine and cytidine derivatives is demonstrated...
March 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28317958/the-collective-behavior-of-spring-like-motifs-tethered-to-a-dna-origami-nanostructure
#4
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/28300237/modular-synthesis-of-supramolecular-dna-amphiphiles-through-host-guest-interactions-and-their-self-assembly-into-dna-decorated-nanovesicles
#5
Shine K Albert, Hari Veera Prasad Thelu, Murali Golla, Nithiyanandan Krishnan, Reji Varghese
DNA nanostructures have found potential applications in various fields including nanotechnology, materials science and nanomedicine, hence the design and synthesis of DNA nanostructures is extremely important. Self-assembly of DNA amphiphiles provides an efficient strategy for the crafting of soft DNA nanostructures. However, the synthesis of DNA amphiphiles is always challenging. Herein, we show a non-covalent approach based on the host-guest interaction between β-CD and adamantane for the synthesis of DNA amphiphiles, and report their amphiphilicity-driven self-assembly into DNA decorated vesicles...
March 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/28295864/block-copolymer-micellization-as-a-protection-strategy-for-dna-origami
#6
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/28290680/4n-1-is-a-sweet-spot-in-dna-i-motif-folding-of-2-deoxycytidine-homopolymers
#7
Aaron M Fleming, Yun Ding, R Aaron Rogers, Judy Zhu, Julia Zhu, Ashlee D Burton, Connor B Carlisle, Cynthia J Burrows
Strands of DNA with four or more contiguous runs of 2'-deoxycytidine (dC) nucleotides have the potential to adopt i-motif folds, generally under mildly acidic conditions. Analysis of dC homo-oligonucleotide strands ranging in length from 10 to 30 nucleotides by five different pH-dependent methods identified a pattern in strand length vs stability. Beginning with dC11, which does not fold, the transition pH (pHT) increased with chain length with the addition of up to four nucleotides, after which the stability dramatically decreased, and the trend repeated this cycle up to dC27...
March 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28287182/dna-conjugated-gold-nanoparticles-based-colorimetric-assay-to-assess-helicase-activity-a-novel-route-to-screen-potential-helicase-inhibitors
#8
Jashmini Deka, Aditya Mojumdar, Pietro Parisse, Silvia Onesti, Loredana Casalis
Helicase are essential enzymes which are widespread in all life-forms. Due to their central role in nucleic acid metabolism, they are emerging as important targets for anti-viral, antibacterial and anti-cancer drugs. The development of easy, cheap, fast and robust biochemical assays to measure helicase activity, overcoming the limitations of the current methods, is a pre-requisite for the discovery of helicase inhibitors through high-throughput screenings. We have developed a method which exploits the optical properties of DNA-conjugated gold nanoparticles (AuNP) and meets the required criteria...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28281339/extracting-the-shape-and-size-of-biomolecules-attached-to-a-surface-as-suspended-discrete-nano-particles
#9
Dimitra Milioni, Achilleas Tsortos, Marisela Vélez, Electra Gizeli
The ability to derive information on the conformation of surface attached biomolecules by using simple techniques such as biosensors is currently considered of great importance in the fields of surface science and nanotechnology. Here we present a nano-shape sensitive biosensor where a simple mathematical expression is used to relate acoustic measurements to the geometrical features of a surface-attached biomolecule. The underlying scientific principle is that the acoustic ratio (ΔD/ΔF) is a measure of the hydrodynamic volume of the attached entity, mathematically expressed by its intrinsic viscosity [η]...
March 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28275219/intrinsic-dynamics-analysis-of-a-dna-octahedron-by-elastic-network-model
#10
Guang Hu, Lei He, Federico Iacovelli, Mattia Falconi
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis...
January 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28265875/the-study-of-mechanisms-of-biological-activity-of-copper-oxide-nanoparticle-cuo-in-the-test-for-seedling-roots-of-triticum-vulgare
#11
Anastasia Mickhailovna Korotkova, Svyatoslav Valeryevich Lebedev, Irina Aleksandrovna Gavrish
The rapid development of nanotechnology raises questions assessment of their impact on living objects. In the present study, we evaluated the impact of nanoparticle (NP) CuO at concentrations ranging from 0.8 to 63.5 g/l in the test on wheat seedlings Triticum vulgare during 1-72 h. In the viability test (WST-test), cells were isolated from the roots of seedlings T. vulgare, 12 h not observed increase reductase activity after 24 h decreased rate of not more than 19% compared with the control. The number of dead cells in seedlings of T...
March 6, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28261325/technical-advances-in-global-dna-methylation-analysis-in-human-cancers
#12
REVIEW
Basudev Chowdhury, Il-Hoon Cho, Joseph Irudayaraj
Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28252973/dna-with-ionic-atomic-and-clustered-silver-an-xps-study
#13
Ivan L Volkov, Anastasiya Smirnova, Anna A Makarova, Zakhar V Reveguk, Ruslan R Ramazanov, Dmitry Yu Usachov, Vera K Adamchuk, Alexei I Kononov
The rapidly developing field of bionanotechnology requires detailed knowledge of the mechanisms of interaction between inorganic matter and biomolecules. Under conditions different from those in an aqueous solution, however, the chemistry of these systems is elusive and may differ dramatically from their interactions in vitro and in vivo. Here, we report for the first time a photoemission study of a metal silver-DNA interface, formed in vacuo, in comparison with DNA-Ag(+) and fluorescent DNA-Ag complexes formed in solution...
March 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28248486/stimuli-responsive-dna-based-hydrogels-from-basic-principles-to-applications
#14
Jason S Kahn, Yuwei Hu, Itamar Willner
The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology...
March 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28214670/metal-mediated-dna-assembly-with-ligand-based-nucleosides
#15
REVIEW
Soham Mandal, Jens Müller
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids...
February 17, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28207239/analyzing-dna-nanotechnology-a-call-to-arms-for-the-analytical-chemistry-community
#16
Divita Mathur, Igor L Medintz
In order to fully realize the potential of DNA nanotechnology, it is crucial to overcome the lack of robust analytical techniques that continue to hinder the purification and characterization of DNA-based structures. In this Feature, we provide a snapshot of the current state of metrological techniques in DNA nanotechnology and look forward to emerging technologies that may offer new ways to probe and visualize these complex structures.
February 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193038/sheathless-focusing-and-separation-of-diverse-nanoparticles-in-viscoelastic-solutions-with-minimized-shear-thinning
#17
Chao Liu, Baoquan Ding, Chundong Xue, Yu Tian, Guoqing Hu, Jiashu Sun
Viscoelastic microfluidics becomes an efficient and label-free hydrodynamic technology to enrich and separate micrometer-scale particles, including blood cells, circulating tumor cells, and bacteria. However, the manipulation of nanoscale particles by viscoelastic microfluidics remains a major challenge, because the viscoelastic force acting on the smaller particle decreases dramatically. In contrast to the commonly used polymer solutions of high molecular weight, herein we utilize the aqueous solutions of poly(ethylene oxide) (PEO) of low molecular weight with minimized shear thinning but sufficient elastic force for high-quality focusing and separation of various nanoparticles...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28185961/non-viral-vectors-based-on-magnetoplexes-lipoplexes-and-polyplexes-for-vegf-gene-delivery-into-central-nervous-system-cells
#18
Ilia Villate-Beitia, Gustavo Puras, Cristina Soto-Sánchez, Mireia Agirre, Edilberto Ojeda, Jon Zarate, Eduardo Fernández, José Luis Pedraz
Nanotechnology based non-viral vectors hold great promise to deliver therapeutic genes into the central nervous system (CNS) in a safe and controlled way. Vascular endothelial growth factor (VEGF) is a potential therapeutic gene candidate for CNS disorders due to its specific roles in brain angiogenesis and neuroprotection. In this work, we elaborated three different non-viral vectors based on magnetic, cationic lipid and polymeric nanoparticles complexed to the phVEGF165aIRESGFP plasmid, which codifies the VEGF protein -extracellular- and the green fluorescent protein (GFP) -intracellular-...
February 6, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28185115/the-sugar-coarse-grained-dna-model
#19
N A Kovaleva, I P Koroleva Kikot, M A Mazo, E A Zubova
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules...
February 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28159697/engineered-nanoparticles-of-titanium-dioxide-tio2-uptake-and-biological-effects-in-a-sea-bass-cell-line
#20
S Picchietti, C Bernini, V Stocchi, A R Taddei, R Meschini, A M Fausto, L Rocco, F Buonocore, D Cervia, G Scapigliati
With the rapid development of nanotechnology there has been a corresponding increase in the application of titanium dioxide nanoparticles (TiO2-NPs) in various consumer and industrial products, consequently their potential health hazards and environmental effects are considered an aspect of great concern. In the present study, in order to assess the impact of TiO2-NPs in the marine environment, the biological effects of TiO2-NPs on a sea bass cell line (DLEC) were investigated. Cells were exposed for 24 h to different concentrations of TiO2-NPs (1, 8, 40, 200 and 1000 μg/ml) or co-exposed with CdCl2 (Cd)...
February 1, 2017: Fish & Shellfish Immunology
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