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Single molecule microscopy

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https://www.readbyqxmd.com/read/28441775/progress-in-the-correlative-atomic-force-microscopy-and-optical-microscopy
#1
REVIEW
Lulu Zhou, Mingjun Cai, Ti Tong, Hongda Wang
Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed...
April 24, 2017: Sensors
https://www.readbyqxmd.com/read/28437395/global-survey-of-the-immunomodulatory-potential-of-common-drugs
#2
Gregory I Vladimer, Berend Snijder, Nikolaus Krall, Johannes W Bigenzahn, Kilian V M Huber, Charles-Hugues Lardeau, Kumar Sanjiv, Anna Ringler, Ulrika Warpman Berglund, Monika Sabler, Oscar Lopez de la Fuente, Paul Knöbl, Stefan Kubicek, Thomas Helleday, Ulrich Jäger, Giulio Superti-Furga
Small-molecule drugs may complement antibody-based therapies in an immune-oncology setting, yet systematic methods for the identification and characterization of the immunomodulatory properties of these entities are lacking. We surveyed the immumomodulatory potential of 1,402 small chemical molecules, as defined by their ability to alter the cell-cell interactions among peripheral mononuclear leukocytes ex vivo, using automated microscopy and population-wide single-cell image analysis. Unexpectedly, ∼10% of the agents tested affected these cell-cell interactions differentially...
April 24, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28437075/fluorescent-photoswitchable-diarylethenes-for-biolabeling-and-single-molecule-localization-microscopies-with-optical-superresolution
#3
Benoit Roubinet, Michael Weber, Heydar Shojaei, Mark Bates, Mariano L Bossi, Vladimir N Belov, Masahiro Irie, Stefan W Hell
A modular assembly of water soluble diarylethenes (DAEs), applicable as bio-markers for optical nanoscopy, is reported. Reversibly photoswitchable 1,2-bis(2-alkyl-6-phenyl-1-benzothiophene-1,1-dioxide-3-yl)perfluorocyclopentenes possessing a fluorescent "closed" form were decorated with one or two methoxy group(s) attached to the para-position(s) of phenyl ring(s) and two, four or eight carboxylic acid groups. Antibody conjugates of these DAEs feature low aggregation, efficient photoswitching in aqueous buffers, specific staining of cellular structures and photophysical properties (high emission efficiencies and low cycloreversion quantum yields) enabling their application in superresolution microscopy...
April 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28434999/smfret-experiments-of-the-rna-polymerase-ii-transcription-initiation-complex
#4
REVIEW
Nicole Malkusch, Thilo Dörfler, Julia Nagy, Tobias Eilert, Jens Michaelis
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET(1)) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28428992/dynamic-shear-force-microscopy-of-confined-liquids-at-a-gold-electrode
#5
Günther Krämer, Florian Hausen, Roland Bennewitz
The confinement of liquids in nanometer-scale gaps can lead to changes in their viscous shear properties. For liquids of polar molecules, the charge state of the confining surfaces has a significant influence on the structure in the confined liquid. Here we report on the implementation of dynamic shear force microscopy in an electrochemical cell. Lateral oscillations of the tip of an atomic force microscope were magnetically activated at a frequency of about 50 kHz. The damping of the lateral tip oscillation was recorded as a function of the tip-sample distance and of the electrode potential at the surface of a Au(100) single crystal electrode...
April 21, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#6
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28426053/improved-spatial-resolution-for-spot-sampling-in-thermal-desorption-atomic-force-microscopy-mass-spectrometry-via-rapid-heating-functions
#7
Suhas Somnath, Stephen Jesse, Gary J Van Berkel, Sergei V Kalinin, Olga S Ovchinnikova
The key to advancing materials is to understand and control their structure and chemistry. However, thorough chemical characterization is challenging since existing techniques characterize only a few properties of the specimen, thereby necessitating multiple measurement platforms to acquire the necessary information. The multimodal combination of atomic force microscopy (AFM) and mass spectrometry (MS) transcends existing analytical capabilities for nanometer scale spatially resolved correlation of the chemical and physical properties of a sample surface...
April 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28426025/modular-low-light-microscope-for-imaging-cellular-bioluminescence-and-radioluminescence
#8
Tae Jin Kim, Silvan Türkcan, Guillem Pratx
Low-light microscopy methods are receiving increased attention as new applications have emerged. One such application is to allow longitudinal imaging of light-sensitive cells with no phototoxicity and no photobleaching of fluorescent biomarkers. Another application is for imaging signals that are inherently dim and undetectable using standard microscopy techniques, such as bioluminescence, chemiluminescence or radioluminescence. In this protocol, we provide instructions on how to build a modular low-light microscope (1-4 d) by coupling two microscope objective lenses, back to back from each other, using standard optomechanical components...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28424742/fret-from-single-to-multiplexed-signaling-events
#9
REVIEW
Gertrude Bunt, Fred S Wouters
Förster resonance energy transfer (FRET) is a powerful tool for the visualization of molecular signaling events such as protein activities and interactions in cells. In its different implementations, FRET microscopy has been mainly used for monitoring single events. Recently, there has been a trend of extending FRET imaging towards the simultaneous detection of multiple events and interactions. The concomitant increase in experimental complexity requires a deeper understanding of the biophysical background of FRET...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424513/super-multiplex-vibrational-imaging
#10
Lu Wei, Zhixing Chen, Lixue Shi, Rong Long, Andrew V Anzalone, Luyuan Zhang, Fanghao Hu, Rafael Yuste, Virginia W Cornish, Wei Min
The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28424492/teststorm-versatile-simulator-software-for-multimodal-super-resolution-localization-fluorescence-microscopy
#11
Tibor Novák, Tamás Gajdos, József Sinkó, Gábor Szabó, Miklós Erdélyi
Optimization of sample, imaging and data processing parameters is an essential task in localization based super-resolution microscopy, where the final image quality strongly depends on the imaging of single isolated fluorescent molecules. A computational solution that uses a simulator software for the generation of test data stacks was proposed, developed and tested. The implemented advanced physical models such as scalar and vector based point spread functions, polarization sensitive detection, drift, spectral crosstalk, structured background etc...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28416636/p53-dynamically-directs-tfiid-assembly-on-target-gene-promoters
#12
R A Coleman, Z Qiao, S K Singh, C S Peng, M Cianfrocco, Z Zhang, A Piasecka, H Aldeborgh, G Basishvili, W L Liu
p53 is a central regulator that turns on vast gene networks to maintain cellular integrity upon various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key question, we have undertaken an integrated approach involving single molecule fluorescence microscopy, single particle cryo-electron microscopy, and biochemistry...
April 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28411855/single-molecule-force-spectroscopy-for-in-situ-probing-oridonin-inhibited-ros-mediated-egf-egfr-interactions-in-living-kyse-150-cells
#13
Jiang Pi, Hua Jin, Jinhuan Jiang, Fen Yang, Huaihong Cai, Peihui Yang, Jiye Cai, Zheng W Chen
As the active anticancer component of Rabdosia Rubescens, oridonin has been proved to show strong anticancer activity in cancer cells, which is also found to be closely related to its specific inhibition effects on the EGFR tyrosine kinase activity. In this study, atomic force microscopy based single molecule force spectroscopy (AFM-SMFS) was used for real-time and in-situ detection of EGF-EGFR interactions in living esophageal cancer KYSE-150 cells to evaluate the anticancer activity of oridonin for the first time...
May 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28406169/single-molecule-electrical-contacts-on-silicon-electrodes-under-ambient-conditions
#14
Albert C Aragonès, Nadim Darwish, Simone Ciampi, Fausto Sanz, J Justin Gooding, Ismael Díez-Pérez
The ultimate goal in molecular electronics is to use individual molecules as the active electronic component of a real-world sturdy device. For this concept to become reality, it will require the field of single-molecule electronics to shift towards the semiconducting platform of the current microelectronics industry. Here, we report silicon-based single-molecule contacts that are mechanically and electrically stable under ambient conditions. The single-molecule contacts are prepared on silicon electrodes using the scanning tunnelling microscopy break-junction approach using a top metallic probe...
April 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28405661/small-molecule-induced-poly-a-single-strand-to-self-structure-conformational-switching-evidence-for-the-prominent-role-of-h-bonding-interactions
#15
Sabyasachi Chatterjee, Gopinatha Suresh Kumar
All messenger RNAs (mRNAs) have a polyadenylic acid tail that is added during post transcriptional RNA processing. Investigation of the structure-function and interactions of polyadenylic acid is an important area to target for cancer and related diseases. Jatrorrhizine and coptisine are two important isoquinoline alkaloids that are structurally very similar, differing only in the substituents on the isoquinoline chromophore. Here we demonstrate that these alkaloids differentially induce a self-structure in single stranded poly(A) using absorbance, thermal melting and differential scanning calorimetry experiments...
April 13, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28402886/three-dimensional-super-resolution-in-eukaryotic-cells-using-the-double-helix-point-spread-function
#16
Alexander R Carr, Aleks Ponjavic, Srinjan Basu, James McColl, Ana Mafalda Santos, Simon Davis, Ernest D Laue, David Klenerman, Steven F Lee
Single-molecule localization microscopy, typically based on total internal reflection illumination, has taken our understanding of protein organization and dynamics in cells beyond the diffraction limit. However, biological systems exist in a complicated three-dimensional environment, which has required the development of new techniques, including the double-helix point spread function (DHPSF), to accurately visualize biological processes. The application of the DHPSF approach has so far been limited to the study of relatively small prokaryotic cells...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402875/tracking-low-copy-transcription-factors-in-living-bacteria-the-case-of-the-lac-repressor
#17
Federico Garza de Leon, Laura Sellars, Mathew Stracy, Stephen J W Busby, Achillefs N Kapanidis
Transcription factors control the expression of genes by binding to specific sites in DNA and repressing or activating transcription in response to stimuli. The lac repressor (LacI) is a well characterized transcription factor that regulates the ability of bacterial cells to uptake and metabolize lactose. Here, we study the intracellular mobility and spatial distribution of LacI in live bacteria using photoactivated localization microscopy combined with single-particle tracking. Since we track single LacI molecules in live cells by stochastically photoactivating and observing fluorescent proteins individually, there are no limitations on the copy number of the protein under study; as a result, we were able to study the behavior of LacI in bacterial strains containing the natural copy numbers (∼40 monomers), as well as in strains with much higher copy numbers due to LacI overexpression...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28402112/self-assembled-upconversion-nanoparticle-clusters-for-nir-controlled-drug-release-and-synergistic-therapy-after-conjugation-with-gold-nanoparticles
#18
Huijuan Cai, Tingting Shen, Alexander M Kirillov, Yu Zhang, Changfu Shan, Xiang Li, Weisheng Liu, Yu Tang
Fabricated three-dimensional (3D) upconversion nanoclusters (abbreviated as EBSUCNPs) are obtained via an emulsion-based bottom-up self-assembly of NaGdF4:Yb/Er@NaGdF4 nanoparticles (abbreviated as UCNPs), which comprise a NaGdF4:Yb/Er core and a NaGdF4 shell. The EBSUCNPs were then coated with a thin mesoporous amino-functionalized SiO2 shell (resulting in EBSUCNPs@SiO2 precursor) and further conjugated with gold nanoparticles to give the novel EBSUCNPs@SiO2@Au material. Finally, EBSUCNPs@SiO2@Au was applied as a biocompatible and efficient drug carrier for doxorubicin (DOX), thus giving rise to a multifunctional EBSUCNPs@SiO2-DOX@Au nanocomposite...
April 12, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28401227/in-situ-mrna-isolation-from-a-microfluidic-single-cell-array-using-an-external-afm-nanoprobe
#19
Xuan Li, Yinglei Tao, Do-Hyun Lee, Hemantha K Wickramasinghe, Abraham P Lee
We present an in situ mRNA extraction platform to quantify marker-genes' expression levels of single target cells within high-density microfluidic trapping arrays. This platform enables single-cell transcriptomic analysis to reveal in-depth information of cellular mechanisms and population heterogeneity. Although microfluidic technology enables the automation of single-cell sorting, trapping and identification, most developed microfluidic devices are closed off and prevent single-cell access by external analytical equipment...
April 12, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28399361/photoexcited-state-confinement-in-two-dimensional-crystalline-anthracene-monolayer-at-room-temperature
#20
Masahiro Shibuta, Naoyuki Hirata, Toyoaki Eguchi, Atsushi Nakajima
Organic thin film electronics place a high demand on bottom-up technology to form a two-dimensionally (2D) functional unit consisting of a single molecular crystalline layer bound to a layered structure. As the strong interaction between a substrate and molecules makes it difficult to evaluate the electronic properties of organic films, the nature of electronic excited states has not been elucidated. Here, we study a 2D crystalline anthracene monolayer electronically decoupled by alkanethiolates on a gold substrate using scanning tunneling microscopy and time-resolved two-photon photoemission spectroscopy and unravel the geometric/electronic structures and excited electron dynamics...
April 25, 2017: ACS Nano
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