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https://www.readbyqxmd.com/read/30227136/multiscale-molecular-visualization
#1
REVIEW
Haichao Miao, Tobias Klein, David Kořil, Peter Mindek, Karsten Schatz, M Eduard Gröller, Barbora Kozlíková, Tobias Isenberg, Ivan Viola
We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation...
September 15, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/30225006/5-cga-n-sequence-assisted-ph-controlled-assembly-of-supramolecular-dna-nanostructure
#2
Yuting Yan, Yanwei Cao, Chunsheng Xiao, Yang Li, Xiaoxuan Xiang, Xinhua Guo
Herein, the DNA strands containing 5'-(CGA) n and consecutive guanines are used to construct supramolecular DNA nanostructures that are size-controlled by pH values. Additionally, the introduction of thymine linkers within DNA nanostructures is necessary to maintain the stability of long-sized nanostructures. This work also demonstrates a method for accurately building DNA nanostructures.
August 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/30224671/template-free-2d-particle-fusion-in-localization-microscopy
#3
Hamidreza Heydarian, Florian Schueder, Maximilian T Strauss, Ben van Werkhoven, Mohamadreza Fazel, Keith A Lidke, Ralf Jungmann, Sjoerd Stallinga, Bernd Rieger
Methods that fuse multiple localization microscopy images of a single structure can improve signal-to-noise ratio and resolution, but they generally suffer from template bias or sensitivity to registration errors. We present a template-free particle-fusion approach based on an all-to-all registration that provides robustness against individual misregistrations and underlabeling. We achieved 3.3-nm Fourier ring correlation (FRC) image resolution by fusing 383 DNA origami nanostructures with 80% labeling density, and 5...
September 17, 2018: Nature Methods
https://www.readbyqxmd.com/read/30221004/time-lapse-live-cell-imaging-to-monitor-doxorubicin-release-from-dna-origami-nanostructures
#4
Yun Zeng, Jiajun Liu, Shuo Yang, Wenyan Liu, Liang Xu, Risheng Wang
Self-assembled DNA nanostructures have attracted significant research interest in biomedical applications because of their excellent programmability and biocompatibility. To develop multifunctional drug delivery from DNA nanostructures, considerable key information is still needed for clinical application. Traditional fixed endpoint assays do not reflect the dynamic and heterogeneous responses of cells with regard to drugs, and may lead to the misinterpretation of experimental results. For the first time, an integrated time-lapse live cell imaging system was used to study the cellular internalization and controlled drug release profile of three different shaped DNA origami/doxorubicin (DOX) complexes for three days...
March 21, 2018: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://www.readbyqxmd.com/read/30219956/impedimetric-determination-of-staphylococcal-enterotoxin-b-using-electrochemical-switching-with-dna-triangular-pyramid-frustum-nanostructure
#5
Xiaoye Chen, Xinping Shi, Yun Liu, Lixia Lu, Yichen Lu, Xiong Xiong, Yuanjian Liu, Xiaohui Xiong
An electrochemical switching strategy is presented for the sensitive determination of Staphylococcus enterotoxin B (SEB). It is based on the use of DNA triangular pyramid frustum nanostructure (TPFDNA ) consisting of (a) three thiolated probes, (b) one auxiliary probe, and (c) an aptamer against SEB. The TPFDNA was assembled on the gold electrode, with the SEB aptamer designed on top of the TPFDNA . The electron transfer to hexacyanoferrate acting as an electrochemical probe is strongly inhibited in the TPFDNA -modified electrode...
September 15, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/30212177/x-ray-mediated-release-of-molecules-and-engineered-proteins-from-nanostructure-surfaces
#6
Mengqi Su, Kathryn G Guggenheim, Jennifer Lien, Justin B Siegel, Ting Guo
Many applications call for initiation of chemical reactions with highly penetrating X-rays with nanometer precision and little damage to the surroundings, which is difficult to realize because of low interaction cross-sections between hard X-rays and organic matters. Here, we demonstrate that a combination of computational protein design of single conjugation site green fluorescent proteins and nanomaterial engineering of silica-covered gold nanoparticles can enhance the release efficiencies of proteins from the surface of nanoparticles...
September 13, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30209641/determination-of-hypoxia-inducible-factor-1-by-using-a-ratiometric-colorimetric-test-based-on-click-mediated-growth-of-gold-nanoparticles
#7
Hong Chen, Yan Sun, Yifei Li, Jing Zhao, Ya Cao
The authors describe a significantly improved colorimetric nanoprobe for the determination of transcription factors (TFs). It is making use of click-mediated growth of gold nanoparticles (AuNPs) to amplify the signal-to-noise ratio. Hypoxia-inducible factor-1 (HIF-1) is an important TF that acts as a mediator of cell response to hypoxia. So, the detection of HIF-1 was chosen as the model analyte. Specifically, target HIF-1 is designed to bind to the hypoxia response element within DNA duplex. The click chemistry between the DNA duplex and alkynyl-functionalized AuNPs (AF-AuNPs) is then inhibited because of significant steric hindrance...
September 12, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/30198626/reversible-photocontrol-of-dna-melting-by-visible-light-responsive-f4-coordinated-azobenzene-compounds
#8
Katarzyna Matczyszyn, Marta Dudek, Marco Deiana, Ziemowit Pokladek, Krzysztof Pawlik
Spatiotemporal control over the regulation of intra- and intermolecular motions in naturally occurring systems is systematically studied to expand the toolbox of mechanical operations in multicomponent nanoarchitectures. DNA is ideally suited for programming light-powered processes based on minimalist molecular design. Herein, we show that the noncovalent incorporation of bistable photoswitches into B-like DNA moieties enables to trigger the thermal transition midpoint of the duplexes by converting visible light into directed mechanical work by orchestrating the collective actions of the photoresponsive chromophores and the host DNA nanostructures...
September 10, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/30188727/programmable-metal-semiconductor-nanostructures-for-mrna-modulated-molecular-delivery
#9
Libing Zhang, Sae Rin Jean, Xiyan Li, Tanja Sack, Zongjie Wang, Sharif Ahmed, Gordon Chan, Jagotamoy Das, Alexandre Zaragoza, Edward H Sargent, Shana O Kelley
Cytotoxic chemotherapeutics are important tools for the clinical treatment of a variety of solid tumors. However, their use is often complicated by multidrug resistance that can develop in patients, limiting the potencies of these agents. New strategies are needed to provide versatile systems that can respond to and disable resistance mechanisms. We demonstrate the use of a new family of materials, programmable metal/semiconductor nanostructures, for drug delivery and mRNA sensing in drug-resistant cells. These materials are composed of a central core gold nanoparticle surrounded by a layer of DNA-capped quantum dots...
September 11, 2018: Nano Letters
https://www.readbyqxmd.com/read/30182521/super-resolution-geometric-barcoding-for-multiplexed-mirna-profiling
#10
Weidong Xu, Peng Yin, Mingjie Dai
MicroRNA (miRNA) expression profiles hold promise as biomarkers for diagnostics and prognosis of complex diseases. Here we present a super-resolution fluorescence imaging-based digital profiling method for specific, sensitive, and multiplexed detection of miRNAs. In particular, we applied DNA-PAINT (Point Accumulation for Imaging in Nanoscale Topography) method to implement a super-resolution geometric barcoding scheme for multiplexed single-molecule miRNA capture and digital counting. Using synthetic DNA nanostructures as programmable miRNA capture "nano-array", we demonstrated high-specificity (single nucleotide mismatch discrimination), multiplexed (8-plex, 2 panels) and sensitive measurements on synthetic miRNA samples, as well as applied one 8-plex panel to measure endogenous miRNAs levels in total RNA extract from HeLa cells...
September 5, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/30179510/stochastic-binding-process-of-blunt-end-stacking-of-dna-molecules-observed-by-atomic-force-microscopy
#11
Taito Sekine, Naoki Kanayama, Kazunari Ozasa, Takashi Nyu, Tomohiro Hayashi, Mizuo Maeda
Hydrophobic attraction is often a physical origin of nonspecific and irreversible (uncontrollable) processes observed for colloidal and biological systems, such as aggregation, precipitation, and fouling with biomolecules. On the contrary, blunt-end stacking of complementary DNA duplex chain pairs, which is also mainly driven by hydrophobic interaction, is specific and stable enough to lead to self-assemblies of DNA nanostructures. To understand the reason behind these contradicting phenomena, we measured forces operating between two self-assembled monolayers of duplexed DNA molecules with blunt ends (DNA-SAMs) and analyzed their statistics...
September 17, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/30178301/dnazyme-embedded-hyperbranched-dna-dendrimers-as-signal-amplifiers-for-colorimetric-determination-of-nucleic-acids
#12
Hadi Ravan, Tahereh Fozooni, Mojdeh Amandadi, Hosseinali Sasan, Akram Norouzi
A DNAzyme-embedded hyperbranched DNA dendrimer is used as a colorimetric signal amplifier in an ultrasensitive detection scheme for nucleic acids. The hyperbranched DNA dendrimers were constructed by single-step autonomous self-assembly of three structure-free DNA monomers. A cascade of self-assembly reactions between the first and second strands leads to the formation of linear DNA concatemers containing overhang flank fragments. The third strand, which bears a peroxidase-mimicking DNAzyme domain, serves as a bridge to trigger self-assembly between the first and second strands across the side chain direction...
September 3, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/30176148/four-point-probe-electrical-measurements-on-templated-gold-nanowires-formed-on-single-dna-origami-tiles
#13
Basu R Aryal, Tyler R Westover, Dulashani R Ranasinghe, Diana G Calvopiña, Bibek Uprety, John N Harb, Robert C Davis, Adam T Woolley
Bottom-up nanofabrication is increasingly making use of self-assembled DNA to fabricate nanowires and potential integrated circuits, although yields of such electronic nanostructures are inadequate, as is the ability to reliably make electrical measurements on them. In this paper, we report improved yields and unprecedented conductivity measurements for Au nanowires created on DNA origami tile substrates. We created several different self-assembled Au nanowire arrangements on DNA origami tiles that are approximately 70 nm × 90 nm, through anisotropic growth of Au nanorods attached to specific sites...
September 12, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/30176014/design-and-synthesis-of-a-reconfigurable-dna-accordion-rack
#14
Yeongjae Choi, Hansol Choi, Amos C Lee, Sunghoon Kwon
DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration...
August 15, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/30172322/nanogapped-au-core-au-ag-shell-structures-coupled-with-fe-3-o-4-magnetic-nanoparticles-for-the-detection-of-ochratoxin-a
#15
Baoyi Shao, Xiaoyuan Ma, Sen Zhao, Yan Lv, Xu Hun, Haitao Wang, Zhouping Wang
Contamination of mycotoxins has been a general problem of food safety and afflicts people all around the world. Ochratoxin A (OTA), an abundant and representative food-contaminating mycotoxin, has a detrimental effect on our health. Herein, an ultrasensitive surface-enhanced Raman scattering (SERS) aptasensor was fabricated for OTA detection. Au(core) @Au-Ag(shell) nanogapped nanostructures (Au@Au-Ag NNSs) were coupled with Fe3 O4 magnetic nanoparticles (Fe3 O4 MNPs) by OTA aptamer and its complementary DNA sequence...
November 29, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/30168311/tetrahedral-dna-nanomaterial-regulates-the-biological-behaviors-of-adipose-derived-stem-cells-via-dna-methylation-on-dlg3
#16
Shiyu Lin, Qi Zhang, Tao Zhang, Xiaoru Shao, Yong Li, Sirong Shi, Taoran Tian, Xiawei Wei, Yunfeng Lin
As a simple and classical three-dimensional shape, tetrahedral DNA nanostructures (TDNs) can provide robust properties for better stability and can serve as a versatile platform for biosensing and drug delivery. More in-depth, its safety should be assessed by sensitive detection methods. However, the effect of TDNs at the epigenetic level has not received much attention. Here, DNA methylation alteration in adipose-derived stem cells (ASCs) after exposure to TDNs was comprehensively evaluated. The results from reduced representation bisulfite sequencing, bisulfite-specific polymerase chain reaction, and further gene function analysis revealed that TDNs induced a few differentially methylated regions where negatively correlated gene expressions occur...
September 12, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30165931/single-dosed-genotoxicity-study-of-gold-nanorod-core-silver-shell-nanostructures-by-pig-a-micronucleus-and-comet-assays
#17
Dan Wang, Mo Dan, Yinglu Ji, Xiaochun Wu, Liming Xu, Hairuo Wen
As an increasing number of nanoproducts enter our daily life, their potential health risks have caused widespread concerns and have also promoted studies of nanotoxicity. Among these investigations, the genotoxicity of nanomaterials has attracted more attention. Engineered silver nanorod with gold core and silver shell (Au@Ag NR) was used in this study to investigate the possible genotoxicity and genotoxicity patterns in peripheral lymphocytes and hepatocytes introduced by released Ag+ and the nanoparticle itself by integrating the Pig-a gene, micronucleus, and comet assays...
November 1, 2018: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/30160812/nature-inspired-emerging-chiral-liquid-crystal-nanostructures-from-molecular-self-assembly-to-dna-mesophase-and-nanocolloids
#18
REVIEW
Ling Wang, Augustine M Urbas, Quan Li
Liquid crystals (LCs) are omnipresent in living matter, whose chirality is an elegant and distinct feature in certain plant tissues, the cuticles of crabs, beetles, arthropods, and beyond. Taking inspiration from nature, researchers have recently devoted extensive efforts toward developing chiral liquid crystalline materials with self-organized nanostructures and exploring their potential applications in diverse fields ranging from dynamic photonics to energy and safety issues. In this review, an account on the state of the art of emerging chiral liquid crystalline nanostructured materials and their technological applications is provided...
August 30, 2018: Advanced Materials
https://www.readbyqxmd.com/read/30156821/spatial-regulation-of-biomolecular-interactions-with-a-switchable-trident-shaped-dna-nanoactuator
#19
Chao Xing, Yuqing Huang, Junduan Dai, Lin Zhong, Huimeng Wang, Yuhong Lin, Juan Li, Chun-Hua Lu, Huang-Hao Yang
DNA nanostructures with controllable motions and functions have been used as flexible scaffolds to precisely and spatially organize molecular reactions at the nanoscale. The construction of dynamic DNA nanostructures with site-specifically incorporated functional elements is a critical step toward building nanomachines. Artificial self-assembled DNA nanostructures have also been developed to mimic key biological processes like various small biomolecule- and protein-based functional biochemistry pathways. Here, we report a self-assembled dynamic trident-shaped DNA (TS DNA) nanoactuator, in which biomolecules can be tethered to the three "arms" of the TS DNA nanoactuator...
September 11, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30155716/electrochemiluminescent-carbon-dot-based-determination-of-microrna-21-by-using-a-hemin-g-wire-supramolecular-nanostructure-as-co-reaction-accelerator
#20
Rui Zhang, Anyi Chen, Yanqing Yu, Yaqin Chai, Ying Zhuo, Ruo Yuan
An efficient coreaction accelerator scheme is introduced in an electrochemiluminescence (ECL) based method for sensitive determination of microRNA-21. It is making use of a domino type hemin/G-wire supramolecular DNA nanostructure (where "G-wire" represents a guanine-rich DNA structure) without a base pairing dependence. A glassy carbon electrode was modified with carbon dots (prepared from fullerene) and TiO2 nanoneedles. In the first step, a first hairpin 1 (H1) binds to microRNA-21 to form the hybridized complex in solution...
August 28, 2018: Mikrochimica Acta
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