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DNA nanotechnology

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https://www.readbyqxmd.com/read/29316151/sub-ensemble-monitoring-of-dna-strand-displacement-using-multiparameter-single-molecule-fret
#1
Laura Baltierra-Jasso, Michael Morten, Steven William Magennis
Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of ca. 10 M-1 s-1...
January 5, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/29250325/modern-biotechnology-based-therapeutic-approaches-against-hiv-infection
#2
Muhammad Imran, Yasir Waheed, Ayesha Ghazal, Sajjad Ullah, Sher Zaman Safi, Muhsin Jamal, Muhammad Ali, Muhammad Atif, Muhammad Imran, Farman Ullah
The causative agent of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus (HIV). Since its discovery before 30 years, a number of drugs known as highly active antiretroviral therapy have been developed to suppress the life cycle of the virus at different stages. With the current therapeutic approaches, ending AIDS means providing treatment to 35 million individuals living with HIV for the rest of their lives or until a cure is developed. Additionally, therapy is associated with various other challenges such as potential of drug resistance, toxicity and presence of latent viral reservoir...
December 2017: Biomedical Reports
https://www.readbyqxmd.com/read/29242318/single-stranded-dna-and-rna-origami
#3
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/29239531/dna-synthesis-by-primer-exchange-reaction-cascades
#4
Marcel Hollenstein
The autonomous synthesis of single-stranded DNA molecules of arbitrary size and sequence composition can easily be achieved by Primer Exchange Reaction (PER) cascades. In PER cascades, the sequential polymerase-mediated extension of DNA primers is guided by catalytic hairpins. This highlight presents this method and illustrates its potential for applications in DNA nanotechnology.
December 14, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29237070/rolling-circle-amplification-shows-a-sinusoidal-template-length-dependent-amplification-bias
#5
Bastian Joffroy, Yavuz O Uca, Domen Prešern, Jonathan P K Doye, Thorsten L Schmidt
Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with integer helical turns circularize much more efficiently than those with odd helical half turns due to stronger stacking of duplex ends. Small DNA circles can serve as templates for rolling circle amplification (RCA), which is a common and extremely robust amplification mechanism for nucleic acids...
December 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29232197/dna-based-construction-at-the-nanoscale-emerging-trends-and-applications
#6
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
#7
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/29225179/synthesis-of-novel-benzodioxane-midst-piperazine-moiety-decorated-chitosan-silver-nanoparticle-against-biohazard-pathogens-and-as-potential-anti-inflammatory-candidate-a-molecular-docking-studies
#8
C S Karthik, H M Manukumar, A P Ananda, S Nagashree, K P Rakesh, L Mallesha, Hua-Li Qin, S Umesha, P Mallu, N B Krishnamurthy
Nanoparticles (NPs) are currently being investigated along with the use of biodegradable polymer containing active agents in many areas of medicine for targeted applications. The present study was aimed to synthesize novel compound Benzodioxane midst piperazine (BP) and characterization of a BP decorated chitosan silver nanoparticles (BP*C@AgNPs) and shown effective against hazardous pathogens, and also having anti-inflammatory property. It was further evaluated for molecular docking proofs, and toxicity. The BP*C@AgNPs had spherical shape with size of 36...
December 7, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29224067/multiplexed-targeted-sequencing-for-oxford-nanopore-minion-a-detailed-library-preparation-procedure
#9
Timokratis Karamitros, Gkikas Magiorkinis
MinION is a small form factor sequencer recently retailed by Oxford Nanopore technologies. This lighter-sized USB3.0-interfaced device uses innovative nanotechnology to generate extra-long reads from libraries prepared using only standard molecular biology lab equipment. The flexibility and the portability of the platform makes it ideal for point-of-interest and real-time surveillance applications. However, MinION's limited capacity is not enough for the study of specific targets within larger genomes. Apart from just PCR-amplifying regions of interest, the capture of long reads spanning the edges of known-unknown genomic regions is of great importance for structural studies, such as the identification of mobile elements' integrations sites, bridging over low complexity repetitive regions etc...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29220504/influence-of-thermodynamically-unfavorable-secondary-structures-on-dna-hybridization-kinetics
#10
Hiroaki Hata, Tetsuro Kitajima, Akira Suyama
Nucleic acid secondary structure plays an important role in nucleic acid-nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29219966/gigadalton-scale-shape-programmable-dna-assemblies
#11
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
https://www.readbyqxmd.com/read/29219963/biotechnological-mass-production-of-dna-origami
#12
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/29218341/templated-co-assembly-into-nanorods-of-polyanions-and-artificial-virus-capsid-proteins
#13
A Hernandez-Garcia, M A Cohen Stuart, R de Vries
Recombinant triblock polypeptides C-Sn-B, where C is a 400 amino acid long hydrophilic random coil block, Sn is a multimer of the silk-like octapeptide S = (GAGAGAGQ), and B = K12 is an oligolysine, have previously been shown to encapsulate double stranded DNA into rod-shaped, virus-like particles. In order to gain insight of the co-assembly process, and in order to be able to use these proteins for templating other types of nanorods, we here explore their co-assembly with a range of polyanionic templates: poly(acrylic acids) (PAA) of a wide range of lengths, poly(styrene sulphonate) (PSS) and the stiff anionic polysaccharide xanthan...
December 8, 2017: Soft Matter
https://www.readbyqxmd.com/read/29217658/nucleic-acid-based-nanotechnology-the-ability-of-dna-and-rna-to-fold-into-precise-and-complex-shapes-can-be-exploited-for-applications-both-in-biology-and-electronics
#14
https://www.readbyqxmd.com/read/29216344/prostate-cancer-updates-on-current-strategies-for-screening-diagnosis-and-clinical-implications-of-treatment-modalities
#15
Jing-Yan Tian, Feng-Jun Guo, Guo-You Zheng, Aamir Ahmad
Prostate cancer is the most common cancer in men by way of diagnosis, and a leading cause of cancer-related deaths. Early detection and intervention remains key to its optimum clinical management. This review provides the most updated information on the recent methods of prostate cancer screening, imaging and treatment modalities. Wherever possible, clinical trial data has been supplemented to provide a comprehensive overview of current prostate cancer research and development. Considering the recent success of immunotherapy in prostate cancer, we discuss cell, DNA and viruses based, as well as combinatorial immunotherapeutic strategies in detail...
December 5, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29210156/selective-nascent-polymer-catch-and-release-enables-scalable-isolation-of-multi-kilobase-single-stranded-dna
#16
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
https://www.readbyqxmd.com/read/29209013/dna-nanotechnology-dna-robots-that-sort-cargoes
#17
Wenjie Sun
No abstract text is available yet for this article.
December 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/29209004/dna-nanotechnology-on-command-molecular-trojans
#18
Christof M Niemeyer
No abstract text is available yet for this article.
December 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/29185744/on-the-origin-of-ionic-rectification-in-dna-stuffed-nanopores-the-breaking-and-retrieving-symmetry
#19
Yanan Jiang, Yaping Feng, Jianjian Su, Jingxin Nie, Liuxuan Cao, Lanqun Mao, Lei Jiang, Wei Guo
The discovery of ionic current rectification (ICR) phenomena in synthetic nanofluidic systems elicits broad interest from interdisciplinary fields of chemistry, physics, materials science, and nanotechnology; and thus, boosts their applications in, for example, chemical sensing, fluidic pumping, and energy related aspects. So far, it is generally accepted that the ICR effect stems from the broken symmetry either in the nanofluidic structures, or in the environmental conditions. Although this empirical regularity is supported by numerous experimental and theoretical results, great challenge still remains to precisely figure out the correlation between the asymmetric ion transport properties and the degree of symmetry breaking...
November 29, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29182318/heterochiral-dna-strand-displacement-circuits
#20
Adam M Kabza, Brian E Young, Jonathan T Sczepanski
The absence of a straightforward strategy to interface native D-DNA with its enantiomer L-DNA - oligonucleotides of opposite chirality are incapable of forming contiguous Watson-Crick (WC) base pairs with each other - has enforced a "homochiral" paradigm over the field of dynamic DNA nanotechnology. As a result, chirality, a key intrinsic property of nucleic acids, is often overlooked as a design element for engineering DNA-based devices, potentially limiting the types of behaviors that can be achieved using these systems...
November 28, 2017: Journal of the American Chemical Society
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