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DNA nanotechnology

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https://www.readbyqxmd.com/read/28731332/tuning-the-cavity-size-and-chirality-of-self-assembling-3d-dna-crystals
#1
Chad R Simmons, Fei Zhang, Tara MacCulloch, Nour Eddine Fahmi, Nicholas Stephanopoulos, Yan Liu, Nadrian C Seeman, Hao Yan
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals, and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold...
July 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28730451/using-planar-phi29-prna-three-way-junction-to-control-size-and-shape-of-rna-nanoparticles-for-biodistribution-profiling-in-mice
#2
Farzin Haque, Congcong Xu, Daniel L Jasinski, Hui Li, Peixuan Guo
RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730435/supported-fluid-lipid-bilayer-as-a-scaffold-to-direct-assembly-of-rna-nanostructures
#3
Aleksandra P Dabkowska, Agnes Michanek, Luc Jaeger, Arkadiusz Chworos, Tommy Nylander, Emma Sparr
RNA architectonics offers the possibility to design and assemble RNA into specific shapes, such as nanoscale 3D solids or nanogrids. Combining the minute size of these programmable shapes with precise positioning on a surface further enhances their potential as building blocks in nanotechnology and nanomedicine. Here we describe a bottom-up approach to direct the arrangement of nucleic acid nanostructures by using a supported fluid lipid bilayer as a surface scaffold. The strong attractive electrostatic interactions between RNA polyanions and cationic lipids promote RNA adsorption and self-assembly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28722430/multi-amplified-sensing-of-microrna-by-a-small-dna-fragment-driven-enzymatic-cascade-reaction
#4
Eunjung Kim, Philip D Howes, Spencer W Crowder, Molly M Stevens
Combining technological developments such as nanomaterials, DNA nanotechnology, and functional enzymes has great potential to facilitate next generation high performance molecular diagnostic systems. In this work, we describe a microRNA (miRNA) detection assay that combines target recycling and isothermal amplification in an elegantly designed enzyme-mediated cascade reaction. Target recycling is driven by the action of duplex-specific nuclease (DSN), resulting in highly amplified translation of input miRNA to short output DNA fragments...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#5
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28714559/how-we-make-dna-origami
#6
Klaus F Wagenbauer, Floris A S Engelhardt, Evi K Stahl, Vera K Hechtl, Pierre Stömmer, Fabian Seebacher, Letizia Meregalli, Philip Ketterer, Thomas Gerling, Hendrik Dietz
DNA ORIGAMI has attracted substantial attention since its invention ten years ago due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. While the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality, and preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge...
July 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28714285/dynamic-cooperation-of-hydrogen-binding-and-%C3%AF-stacking-in-ssdna-adsorption-on-graphene-oxide
#7
Zhen Xu, Xiaoling Lei, Yusong Tu, Zhi-Jie Tan, Bo Song, Haiping Fang
Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on a GO surface. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and a π-π stacking interaction, with preferential binding to an oxidized region rather than to an unoxidized region of the GO surface...
July 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28702671/self-assembly-of-porphyrin-dna-hybrids-into-large-flat-nanostructures
#8
G Chatelain, G Clavé, C Saint-Pierre, D Gasparutto, S Campidelli
The main aim of nanotechnology is to create functional systems by controlling the matter at the nanometer level. In this context DNA is a versatile building block for the fabrication of micrometer-scale objects with a subnanometer-scale resolution. Over the last 15 years, DNA nanotechnology has considerably developed with the invention of DNA origami, double crossover structures and molecule/oligonucleotide hybrids. Our interest is focused on the combination of short complementary DNA sequences with organic molecules with a view to create large self-assembled nanostructures...
July 12, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28681897/solid-surface-vs-liquid-surface-nanoarchitectonics-molecular-machines-and-dna-origami
#9
Katsuhiko Ariga, Taizo Mori, Waka Nakanishi, Jonathan P Hill
The investigation of molecules and materials at interfaces is critical for the accumulation of new scientific insights and technological advances in the chemical and physical sciences. Immobilization on solid surfaces permits the investigation of different properties of functional molecules or materials with high sensitivity and high spatial resolution. Liquid surfaces also present important media for physicochemical innovation and insight based on their great flexibility and dynamicity, rapid diffusion of molecular components for mixing and rearrangements, as well as drastic spatial variation in the prevailing dielectric environment...
July 6, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28655200/highly-efficient-preparation-of-single-stranded-dna-rings-by-t4-ligase-at-abnormally-low-mg-ii-concentration
#10
Ran An, Qi Li, Yiqiao Fan, Jing Li, Xiaoming Pan, Makoto Komiyama, Xingguo Liang
Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buffer for ligase reactions. This strategy is based on our unexpected finding that, in diluted T4 buffers, intermolecular polymerization of DNA fragments is greatly suppressed with respect to their intramolecular cyclization...
June 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28652006/3d-nus-a-web-server-for-automated-modeling-and-visualization-of-non-canonical-3-dimensional-nucleic-acid-structures
#11
L Ponoop Prasad Patro, Abhishek Kumar, Narendar Kolimi, Thenmalarchelvi Rathinavelan
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information...
June 23, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28645043/in-vitro-and-in-vivo-behavior-of-dna-tetrahedrons-as-tumor-targeting-nanocarriers-for-doxorubicin-delivery
#12
Ji Hee Kang, Kyoung-Ran Kim, Hyukjin Lee, Dae-Ro Ahn, Young Tag Ko
Deoxyribonucleic acid (DNA) is a versatile material with high applicability and inherent biocompatibility. L-DNA, the perfect mirror form of the naturally occurring D-DNA, has been used in DNA nanotechnology. It has thermodynamically identical properties to D-DNA, is capable of self-assembly and bio-orthogonal base-pairing, and is resistant to nuclease activity. We previously constructed an L-DNA tetrahedron (L-Td) and found that this nanostructure has remarkably higher capacity for cell penetration than its natural counterpart (D-Td)...
June 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28644477/dna-nanotechnology-bringing-lipid-bilayers-into-shape
#13
Stefan Howorka
No abstract text is available yet for this article.
June 23, 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28643452/emerging-nanotechnology-and-advanced-materials-for-cancer-radiation-therapy
#14
REVIEW
Guosheng Song, Liang Cheng, Yu Chao, Kai Yang, Zhuang Liu
Radiation therapy (RT) including external beam radiotherapy (EBRT) and internal radioisotope therapy (RIT) has been widely used for clinical cancer treatment. However, owing to the low radiation absorption of tumors, high doses of ionizing radiations are often needed during RT, leading to severe damages to normal tissues adjacent to tumors. Meanwhile, the RT efficacies are limited by different mechanisms, among which the tumor hypoxia-associated radiation resistance is a well-known one, as there exists hypoxia inside most solid tumors while oxygen is essential to enhance radiation-induced DNA damages...
June 23, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28642488/biomimetic-molecular-signaling-using-dna-walkers-on-microparticles
#15
Tulsi Ram Damase, Adam Spencer, Bamidele Samuel, Peter B Allen
We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using fluorescence barcoding: we synthesized and distinguished multiple particle types with multicolor fluorescence microscopy and automated image analysis software...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628332/watson-crick-base-pair-radical-cation-as-a-model-for-oxidative-damage-in-dna
#16
Linda Feketeová, Bun Chan, George N Khairallah, Vincent Steinmetz, Philippe Maitre, Leo Radom, Richard A J O'Hair
The deleterious cellular effects of ionizing radiation are well-known, but the mechanisms causing DNA damage are poorly understood. The accepted molecular events involve initial oxidation and deprotonation at guanine sites, triggering hydrogen atom abstraction reactions from the sugar moieties, causing DNA strand breaks. Probing the chemistry of the initially formed radical cation has been challenging. Here, we generate, spectroscopically characterize, and examine the reactivity of the Watson-Crick nucleobase pair radical cation in the gas phase...
June 27, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28625157/purification-of-single-stranded-dna-by-co-polymerization-with-acrylamide-and-electrophoresis
#17
Tulsi Ram Damase, Andrew D Ellington, Peter B Allen
Single-stranded DNA (ssDNA) oligonucleotides are useful as aptamers, hybridization probes and for emerging applications in DNA nanotechnology. Current methods to purify ssDNA require both a strand-separation step and a separate size-separation step but may still leave double-stranded DNA (dsDNA) impurities in the sample. Here, we use commercially available acrydite DNA primers to immobilize one strand of a PCR product within a polyacrylamide matrix. Electrophoresis moves the non-crosslinked DNA into the gel where the single-stranded product of desired size can be recovered...
June 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28624216/gold-nanoparticles-for-bcr-abl1-gene-silencing-improving-tyrosine-kinase-inhibitor-efficacy-in-chronic-myeloid-leukemia
#18
Raquel Vinhas, Alexandra R Fernandes, Pedro V Baptista
Introduction of tyrosine kinase inhibitors for chronic myeloid leukemia treatment is associated with a 63% probability of maintaining a complete cytogenetic response, meaning that over 30% patients require an alternative methodology to overcome resistance, tolerance, or side effects. Considering the potential of nanotechnology in cancer treatment and the benefits of a combined therapy with imatinib, a nanoconjugate was designed to achieve BCR-ABL1 gene silencing. Gold nanoparticles were functionalized with a single-stranded DNA oligonucleotide that selectively targets the e14a2 BCR-ABL1 transcript expressed by K562 cells...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28616969/ph-driven-actuation-of-dna-origami-via-parallel-i-motif-sequences-in-solution-and-on-surfaces
#19
Jacob M Majikes, Lucas C C Ferraz, Thomas H LaBean
As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures...
June 27, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28610975/pna-monomers-fully-compatible-with-standard-fmoc-based-solid-phase-synthesis-of-pseudocomplementary-pna
#20
Toru Sugiyama, Genki Hasegawa, Chie Niikura, Keiko Kuwata, Yasutada Imamura, Yosuke Demizu, Masaaki Kurihara, Atsushi Kittaka
Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase...
August 1, 2017: Bioorganic & Medicinal Chemistry Letters
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