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Single molecule microscopy

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https://www.readbyqxmd.com/read/28812314/self-assembled-chiral-nanostructures-of-amphiphilic-peptide-from-single-molecule-to-aggregate
#1
Ting Zhou, Zhiqing Zhang, Xuemei Zhang, Chen Wang, Guiying Xu, Yanlian Yang
We report interesting hierarchical self-assembled architectures from a designed amphiphilic peptide. The bisignate cotton effects in circular dichroism spectra show typical peptide aggregation-induced. The observation of peptide assembly structures from initial particles and fibrils to ribbon structures is supported by microscopy (atomic force microscopy and transmission electron microscopy). The visualization of individual peptide at the single molecular level offered insights of the intermolecular interactions responsible for the formation of aggregates, which is investigated by scanning tunneling microscopy...
August 15, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28809081/diagnosing-the-internal-architecture-of-zeolite-ferrierite
#2
Joel E Schmidt, Frank C Hendriks, Martin Lutz, L Christiaan Post, Donglong Fu, Dr Bert M Weckhuysen
Large crystals of zeolite ferrierite (FER) are important model systems for spatially resolved catalysis and diffusion studies, though there is considerable variation in crystal habit depending on the chemical composition and employed synthesis conditions. A synergistic combination of techniques has been applied, including single crystal X-ray diffraction, high-temperature in situ confocal fluorescence microscopy, fluorescent probe molecules, wide-field microscopy and atomic force microscopy to unravel the internal architecture of three distinct FER zeolites...
August 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28800752/a-type-i-combi-targeting-approach-for-the-design-of-molecules-with-enhanced-potency-against-brca1-2-mutant-and-o6-methylguanine-dna-methyltransferase-mgmt-expressing-tumour-cells
#3
Zhor Senhaji Mouhri, Elliot Goodfellow, Bertrand Jean-Claude
BACKGROUND: Mutations of the DNA repair proteins BRCA1/2 are synthetically lethal with the DNA repair enzyme poly(ADP-ribose) polymerase (PARP), which when inhibited, leads to cell death due to the absence of compensatory DNA repair mechanism. The potency of PARP inhibitors has now been clinically proven. However, disappointingly, acquired resistance mediated by the reactivation of wild type BRCA1/2 has been reported. In order to improve their efficacy, trials are ongoing to explore their combinations with temozolomide (TMZ)...
August 11, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28799330/imaging-dynamic-collision-and-oxidation-of-single-silver-nanoparticles-at-the-electrode-solution-interface
#4
Rui Hao, Yunshan Fan, Bo Zhang
The electrochemical interface is an ultrathin interfacial region between the electrode surface and the electrolyte solution and is often characterized by numerous dynamic processes, such as solvation and desolvation, heterogeneous electron transfer, molecular adsorption and desorption, diffusion, and surface rearrangement. Many of these processes are driven and modulated by the presence of a large interfacial potential gradient. The study and better understanding of the electrochemical interface is important for designing better electrochemical systems where their applications may include batteries, fuel cells, electrocatalytic water splitting, corrosion protection, and electroplating...
August 11, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28798968/stretching-of-surface-tethered-polymers-in-pressure-driven-flow-under-confinement
#5
Tamal Roy, Kai Szuttor, Jens Smiatek, Christian Holm, Steffen Hardt
We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We find that the fractional extension of the tethered DNA molecules mainly depends on the wall shear stress, with effects of confinement being very weak. Experiments performed with molecules of different contour length show that the fractional extension is a universal function of the product of the wall shear stress and the contour length, a result that can be obtained from a simple scaling relation...
August 11, 2017: Soft Matter
https://www.readbyqxmd.com/read/28792742/sequential-release-of-proteins-from-structured-multishell-microcapsules
#6
Ulyana Shimanovich, Thomas C T Michaels, Erwin J de Genst, Dijana Matak-Vinkovic, Christopher M Dobson, Tuomas P J Knowles
In nature, a wide range of functional materials is based on proteins. Increasing attention is also turning to the use of proteins as artificial biomaterials in the form of films, gels, particles and fibrils that offer great potential for applications in areas ranging from molecular medicine to materials science. To date, however, most such applications have been limited to single component materials despite the fact that their natural analogues are composed of multiple types of proteins with a variety of functionalities that are co-assembled in a highly organized manner on the micron scale, a process which is currently challenging to achieve in the laboratory...
August 9, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28782000/particle-segmentation-algorithm-for-flexible-single-particle-reconstruction
#7
Qiang Zhou, Niyun Zhou, Hong-Wei Wang
As single particle cryo-electron microscopy has evolved to a new era of atomic resolution, sample heterogeneity still imposes a major limit to the resolution of many macromolecular complexes, especially those with continuous conformational flexibility. Here, we describe a particle segmentation algorithm towards solving structures of molecules composed of several parts that are relatively flexible with each other. In this algorithm, the different parts of a target molecule are segmented from raw images according to their alignment information obtained from a preliminary 3D reconstruction and are subjected to single particle processing in an iterative manner...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28779837/single-molecule-fluorescence-studies-of-membrane-transporters-using-total-internal-reflection-microscopy
#8
Joris M H Goudsmits, Antoine M van Oijen, Dirk J Slotboom
Cells are delineated by a lipid bilayer that physically separates the inside from the outer environment. Most polar, charged, or large molecules require proteins to reduce the energetic barrier for passage across the membrane and to achieve transport rates that are relevant for life. Here, we describe techniques to visualize the functioning of membrane transport proteins with fluorescent probes at the single-molecule level. First, we explain how to produce membrane-reconstituted transporters with fluorescent labels...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28777580/a-first-step-towards-a-universal-fluorescent-probe-unravelling-the-photodynamics-of-an-amino-maleimide-fluorophore
#9
Michael Staniforth, Wen-Dong Quan, Tolga N V Karsili, Lewis A Baker, Rachel K O'Reilly, Vasilios G Stavros
Continuous advancements in biophysics and medicine at the molecular level make the requirements to image structure-function processes in living cells ever more acute. While fluorophores such as the green fluorescent protein have proven instrumental towards such efforts, the advent of non-diffraction limited microscopy limits the utility of such fluorescent tags. Monoaminomaleimides are small, single molecule fluorophores that have been shown to possess stark variations in their emission spectra in different solvent environments, making them a potentially powerful tool for myriad applications...
August 4, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28777541/uv-curable-contact-active-benzophenone-terminated-quaternary-ammonium-antimicrobials-for-applications-in-polymer-plastics-and-related-devices
#10
Lukas Porosa, Alexander Caschera, Amanda Mocella, Joseph Bedard, Evan Ronan, Alan J Lough, Gideon Wolfaardt, Daniel Foucher
A series of UV active benzophenone ([C6H5COC6H4-O-(CH2)n-N+Me2R][X-], 4: R = C12H25, n = 3, X- = Br- , 5a-c: R = C18H37, n = 3, X- = Cl-, Br-, I-; 6a-c: R = C18H37, n = 4, X- = Cl-, Br-, I- ; 7a-c: R = C18H37, n = 6, X- = Cl-, Br-, I-) terminated C12 and C18 quaternary ammonium salts (QACs) were prepared by thermal or microwave driven Menshutkin protocols of the appropriate benzophenone alkyl halide (1a-c, 2a-c, 3a-c) with the corresponding dodecyl- or octadecyl N,N-dimethylamine. All new compounds were characterized by NMR spectroscopy, HRMS spectrometry and in one instance (4) by single crystal X-ray crystallography...
August 4, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28775267/ectoine-can-enhance-structural-changes-in-dna-in-vitro
#11
S Meyer, M-A Schröter, M B Hahn, T Solomun, H Sturm, H J Kunte
Strand breaks and conformational changes of DNA have consequences for the physiological role of DNA. The natural protecting molecule ectoine is beneficial to entire bacterial cells and biomolecules such as proteins by mitigating detrimental effects of environmental stresses. It was postulated that ectoine-like molecules bind to negatively charged spheres that mimic DNA surfaces. We investigated the effect of ectoine on DNA and whether ectoine is able to protect DNA from damages caused by ultraviolet radiation (UV-A)...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28774176/spectrally-resolved-functional-super-resolution-microscopy-reveals-nanoscale-compositional-heterogeneity-in-live-cell-membranes
#12
Seonah Moon, Rui Yan, Samuel J Kenny, Yennie Shyu, Limin Xiang, Wan Li, Ke Xu
By recording the full fluorescence spectra and super-resolved positions of ∼10(6) individual polarity-sensing solvatochromic molecules, we reveal compositional heterogeneity in the membranes of live mammalian cells with single-molecule sensitivity and ∼30 nm spatial resolution. This allowed us to unveil distinct polarity characteristics of the plasma membrane and the membranes of nanoscale intracellular organelles, a result we found to be due to differences in cholesterol levels. Within the plasma membrane, we observed the formation of low-polarity, raft-like nanodomains upon cholesterol addition or cholera-toxin treatment, but found this nanoscale phase separation absent in native cells...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28772831/preparation-characterization-and-application-of-a-molecularly-imprinted-polymer-for-selective-recognition-of-sulpiride
#13
Wei Zhang, Xuhui She, Liping Wang, Huajun Fan, Qing Zhou, Xiaowen Huang, James Z Tang
A novel molecular imprinting polymer (MIP) was prepared by bulk polymerization using sulpiride as the template molecule, itaconic acid (ITA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the crosslinker. The formation of the MIP was determined as the molar ratio of sulpiride-ITA-EGDMA of 1:4:15 by single-factor experiments. The MIP showed good adsorption property with imprinting factor α of 5.36 and maximum adsorption capacity of 61.13 μmol/g, and was characterized by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR) and surface area analysis...
April 28, 2017: Materials
https://www.readbyqxmd.com/read/28772365/dysprosium-acetylacetonato-single-molecule-magnet-encapsulated-in-carbon-nanotubes
#14
Ryo Nakanishi, Mudasir Ahmad Yatoo, Keiichi Katoh, Brian K Breedlove, Masahiro Yamashita
Dy single-molecule magnets (SMMs), which have several potential uses in a variety of applications, such as quantum computing, were encapsulated in multi-walled carbon nanotubes (MWCNTs) by using a capillary method. Encapsulation was confirmed by using transmission electron microscopy (TEM). In alternating current magnetic measurements, the magnetic susceptibilities of the Dy acetylacetonato complexes showed clear frequency dependence even inside the MWCNTs, meaning that this hybrid can be used as magnetic materials in devices...
December 23, 2016: Materials
https://www.readbyqxmd.com/read/28768714/kinetics-of-crpv-and-hcv-ires-mediated-eukaryotic-translation-using-single-molecule-fluorescence-microscopy
#15
Olivier Bugaud, Nathalie Barbier, Hélène Chommy, Nicolas Fiszman, Antoine Le Gall, David Dullin, Matthieu Saguy, Nathalie Westbrook, Karen Perronet, Olivier Namy
Protein synthesis is a complex multi-step process involving many factors that need to interact in a coordinated manner to properly translate the messenger RNA. As translating ribosomes cannot be synchronized over many elongation cycles, single molecule studies have been introduced to bring a deeper understanding of prokaryotic translation dynamics. Extending this approach to eukaryotic translation is very appealing, but initiation and specific labelling of the ribosomes are much more complicated. Here we use a non-canonical translation initiation based on internal ribosome entry sites (IRES) and we monitor the passage of individual, unmodified mammalian ribosomes at specific fluorescent milestones along mRNA...
August 2, 2017: RNA
https://www.readbyqxmd.com/read/28766344/cell-shaping-micropatterns-for-quantitative-super-resolution-microscopy-imaging-of-membrane-mechanosensing-proteins
#16
Anthony Fernandez, Markville Bautista, Ramunas Stanciauskas, Taerin Chung, Fabien Pinaud
Patterning cells on microcontact-printed substrates is a powerful approach to control cell morphology and introduce specific mechanical cues on a cell's molecular organization. Although global changes in cellular architectures caused by micropatterns can easily be probed with diffraction-limited optical microscopy, studying molecular reorganizations at the nanoscale demands micropatterned substrates that accommodate the optical requirements of single molecule microscopy techniques. Here, we developed a simple micropatterning strategy that provides control of cellular architectures and is optimized for nanometer accuracy single molecule tracking and three-dimensional super-resolution imaging of plasma and nuclear membrane proteins in cells...
August 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28762410/accurate-nanoscale-flexibility-measurement-of-dna-and-dna-protein-complexes-by-atomic-force-microscopy-in-liquid
#17
Divakaran Murugesapillai, Serge Bouaziz, L James Maher, Nathan E Israeloff, Craig E Cameron, Mark C Williams
The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model. This often results in a persistence length measurement that is different from the value determined using bulk and single molecule methods...
August 1, 2017: Nanoscale
https://www.readbyqxmd.com/read/28762198/directly-watching-biomolecules-in-action-by-high-speed-atomic-force-microscopy
#18
REVIEW
Toshio Ando
Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, high-speed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions...
July 31, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28756663/design-and-characterization-of-an-electrically-powered-single-molecule-on-gold
#19
Rémy Pawlak, Tobias Meier, Nicolas Renaud, Marcin Kisiel, Antoine Hinaut, Thilo Glatzel, Delphine Sordes, Corentin Durand, We-Hyo Soe, Alexis Baratoff, Christian Joachim, Catherine Elizabeth Housecroft, Edwin C Constable, Ernst Meyer
The surface diffusion of individual molecules is of paramount importance in self-assembly processes and catalytic processes. However, the fundamental understanding of molecule diffusion peculiarities considering conformations and adsorption sites remain poorly known at the atomic-scale. Here, we probe 4'-(4-tolyl)-2,2':6',2"-terpyridine adsorbed on the Au(111) herringbone structure combining scanning tunneling microscopy and atomic force microscopy. Molecules are controllably translated by electrons excitations over the reconstruction, except at elbows acting as pinning centres...
July 30, 2017: ACS Nano
https://www.readbyqxmd.com/read/28756025/direct-observation-of-positive-supercoils-introduced-by-reverse-gyrase-through-atomic-force-microscopy
#20
Dawei Li, Bei Lv, Qiang Wang, Yun Liu, Qiang Zhuge
Reverse gyrase is a hyperthermophilic enzyme that can introduce positive supercoiling in substrate DNA. It is showed in our studies that positive DNA supercoils were induced in both pBR322 vector and an artificially synthesized mini-plasmid DNA by reverse gyrase. The left-handed structures adopted by positively supercoiled DNA molecules could be identified from their right-handed topoisomers through atomic force microscopic examination. Additional structural comparisons revealed that positively supercoiled DNA molecule AFM images exhibited increased contour lengths...
July 15, 2017: Bioorganic & Medicinal Chemistry Letters
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