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Single molecule microscopy

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https://www.readbyqxmd.com/read/29351274/dna-polymerase-iv-primarily-operates-outside-of-dna-replication-forks-in-escherichia-coli
#1
Sarah S Henrikus, Elizabeth A Wood, John P McDonald, Michael M Cox, Roger Woodgate, Myron F Goodman, Antoine M van Oijen, Andrew Robinson
In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates...
January 19, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29350516/time-dependent-density-functional-theory-for-open-systems-and-its-applications
#2
Shuguang Chen, YanHo Kwok, GuanHua Chen
Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom...
January 19, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29348232/a-self-assembled-nanoscale-robotic-arm-controlled-by-electric-fields
#3
Enzo Kopperger, Jonathan List, Sushi Madhira, Florian Rothfischer, Don C Lamb, Friedrich C Simmel
The use of dynamic, self-assembled DNA nanostructures in the context of nanorobotics requires fast and reliable actuation mechanisms. We therefore created a 55-nanometer-by-55-nanometer DNA-based molecular platform with an integrated robotic arm of length 25 nanometers, which can be extended to more than 400 nanometers and actuated with externally applied electrical fields. Precise, computer-controlled switching of the arm between arbitrary positions on the platform can be achieved within milliseconds, as demonstrated with single-pair Förster resonance energy transfer experiments and fluorescence microscopy...
January 19, 2018: Science
https://www.readbyqxmd.com/read/29347432/lattice-diffusion-of-a-single-molecule-in-solution
#4
Francesca Ruggeri, Madhavi Krishnan
The ability to trap a single molecule in an electrostatic potential well in solution has opened up new possibilities for the use of molecular electrical charge to study macromolecular conformation and dynamics at the level of the single entity. Here we study the diffusion of a single macromolecule in a two-dimensional lattice of electrostatic traps in solution. We report the ability to measure both the size and effective electrical charge of a macromolecule by observing single-molecule transport trajectories, typically a few seconds in length, using fluorescence microscopy...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346720/nanoscale-control-of-molecular-self-assembly-induced-by-plasmonic-hot-electron-dynamics
#5
Sabrina Simoncelli, Yi Li, Emiliano Cortes, Stefan A Maier
Self-assembly processes allow designing and creating complex nanostructures using molecules as building blocks and surfaces as scaffolds. This autonomous driven construction is possible due to a complex thermodynamic balance of molecule-surface interactions. As such, nanoscale guidance and control over this process is hard to achieve. Here we use the highly localized light-to-chemical-energy conversion of plasmonic materials to spatially cleave Au-S bonds on pre-determined locations within a single nanoparticle, enabling a high degree of control over this archetypal system for molecular self-assembly...
January 18, 2018: ACS Nano
https://www.readbyqxmd.com/read/29336349/nanodoping-a-route-for-enhancing-electro-optic-performance-of-bent-core-nematic-system
#6
Pradeep Kumar, Somen Debnath, Nandiraju V S Rao, Aloka Sinha
We report the effect of dispersion of barium titanate (BaTiO<sub>3</sub>) nanoparticles (BNPs) in a four ring bent core nematic (BCN) liquid crystal.Polarizing optical microscopy (POM) reveals the presence of a single nematic phase in pure and doped states. Polar switching has been observed in the bent core system and the value of spontaneous polarization (Ps) increases with increase in doping concentration of BNPs in BCN. Dielectric study shows a lower frequency mode, which can be ascribed to the formation of cybotactic clusters...
January 16, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29334219/mussel-inspired-conductive-polymer-binder-for-si-alloy-anode-in-lithium-ion-batteries
#7
Hui Zhao, Yang Wei, Cheng Wang, Rui-Min Qiao, Wanli Yang, Phillip B Messersmith, Gao Liu
The excessive volume changes during cell cycling of Si-based anode in lithium ion batteries impeded its application. One major reason for the cell failure is particle isolation during volume shrinkage in delithiation process, which makes strong adhesion between polymer binder and anode active material particles a highly desirable property. Here, a biomimetic side-chain conductive polymer incorporating catechol, a key adhesive component of the mussel holdfast protein, was synthesized. Atomic force microscopy (AFM) based single molecule force measurements of mussel-inspired conductive polymer binder contacting a silica surface revealed similar adhesion toward substrate when compared with an effective Si anode binder, homo-polyacrylic acid (PAA), with the added benefit of being electronically conductive...
January 15, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29330363/disulfide-isomerization-reactions-in-titin-immunoglobulin%C3%A2-domains-enable-a-mode-of-protein-elasticity
#8
David Giganti, Kevin Yan, Carmen L Badilla, Julio M Fernandez, Jorge Alegre-Cebollada
The response of titin to mechanical forces is a major determinant of the function of the heart. When placed under a pulling force, the unstructured regions of titin uncoil while its immunoglobulin (Ig) domains unfold and extend. Using single-molecule atomic force microscopy, we show that disulfide isomerization reactions within Ig domains enable a third mechanism of titin elasticity. Oxidation of Ig domains leads to non-canonical disulfide bonds that stiffen titin while enabling force-triggered isomerization reactions to more extended states of the domains...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29328231/aberration-accounting-calibration-for-3d-single-molecule-localization-microscopy
#9
Clément Cabriel, Nicolas Bourg, Guillaume Dupuis, Sandrine Lévêque-Fort
We propose a straightforward sample-based technique to calibrate the axial detection in 3D single-molecule localization microscopy. Using microspheres coated with fluorescent molecules, the calibration curves of point spread function-shaping or intensity-based measurements can be obtained over the imaging depth range. This experimental method takes into account the effect of the spherical aberration without requiring computational correction. We demonstrate its efficiency for astigmatic imaging in a 1.2 μm range above the coverslip...
January 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29320677/warhammers-for-peaceful-times
#10
Piotr E Marszalek
The Perkins group has recently developed a number of improved atomic force microscopy cantilevers using the focused ion beam technology. They compared the performance of these cantilevers in "real-life" biophysical single-molecule force spectroscopy measurements on protein unfolding, and the results of this comparison are reported in this issue of Biophysical Journal.
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29319220/drug-induced-micelle-to-vesicle-transition-of-a-cationic-gemini-surfactant-potential-applications-in-drug-delivery
#11
Sargam M Rajput, Sugam Kumar, Vinod K Aswal, Omar El Seoud, Naved Anjum I Malek, Suresh Kumar Kailasa
The impetus for the sustained interest in the formation of vesicles is their potential application as efficient drug delivery systems. A simple approach for ionic surfactants is to add a vesicle-inducing drug of opposite charge. In ionic gemini surfactants (GS) two molecules are covalently linked with a "spacer". Considering drug-delivery, GS are more attractive candidates than their single-chain counterparts because of their high surface activity and the effect on the physico-chemical properties of their solutions caused by changing the length of the spacer, and inclusion of heteroatoms therein...
January 10, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/29318250/razor-printed-sticker-microdevices-for-cell-based-applications
#12
Loren E Stallcop, Yasmín R Álvarez-García, Ana M Reyes-Ramos, Karla P Ramos-Cruz, Molly M Morgan, Yatao Shi, Lingjun Li, David J Beebe, Maribella Domenech, Jay W Warrick
Tape-based razor-printing is a flexible and affordable ultra-rapid prototyping approach for microscale device fabrication. However, integration of this prototyping approach into cell-based assay development has been limited to proof of principle demonstrations. This is in large part due to lack of an established or well-characterized option for biocompatible adhesive tape. Without such an option, integration of these areas will remain unexplored. Therefore, to address this critical hurdle, we characterized microscale devices made using a potentially biocompatible double-sided adhesive, ARCare 90106...
January 10, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29317715/hybtrack-a-hybrid-single-particle-tracking-software-using-manual-and-automatic-detection-of-dim-signals
#13
Byung Hun Lee, Hye Yoon Park
Single particle tracking is a compelling technique for investigating the dynamics of nanoparticles and biological molecules in a broad range of research fields. In particular, recent advances in fluorescence microscopy have made single molecule tracking a prevalent method for studying biomolecules with a high spatial and temporal precision. Particle tracking algorithms have matured over the past three decades into more easily accessible platforms. However, there is an inherent difficulty in tracing particles that have a low signal-to-noise ratio and/or heterogeneous subpopulations...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317629/3d-single-molecule-super-resolution-microscopy-with-a-tilted-light-sheet
#14
Anna-Karin Gustavsson, Petar N Petrov, Maurice Y Lee, Yoav Shechtman, W E Moerner
Tilted light sheet microscopy with 3D point spread functions (TILT3D) combines a novel, tilted light sheet illumination strategy with long axial range point spread functions (PSFs) for low-background, 3D super-localization of single molecules as well as 3D super-resolution imaging in thick cells. Because the axial positions of the single emitters are encoded in the shape of each single-molecule image rather than in the position or thickness of the light sheet, the light sheet need not be extremely thin. TILT3D is built upon a standard inverted microscope and has minimal custom parts...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29313112/size-extensivity-of-elastic-properties-of-alkane-fragments
#15
Milad Radiom, Plinio Maroni, Tomasz A Wesolowski
Using MP2, CCSD, and B3LYP methods of computational chemistry, we show length dependence in the intrinsic elastic properties of short alkane fragments. For isolated alkane fragments of finite length in the gas phase and zero temperature, the intrinsic elasticity constants are found to vary with the number of carbon atoms and its parity. From extrapolation of the elasticity constants calculations to infinite chain length, and by comparing with in-situ elasticity constant of single poly(ethylene) molecule obtained with atomic force microscopy, we estimate the softening effect of environment on the extension response of the polymer...
January 8, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29309696/single-molecule-localization-microscopy-reveals-molecular-transactions-during-rad51-filament-assembly-at-cellular-dna-damage-sites
#16
Kalina T Haas, MiYoung Lee, Alessandro Esposito, Ashok R Venkitaraman
RAD51 recombinase assembles on single-stranded (ss)DNA substrates exposed by DNA end-resection to initiate homologous recombination (HR), a process fundamental to genome integrity. RAD51 assembly has been characterized using purified proteins, but its ultrastructural topography in the cell nucleus is unexplored. Here, we combine cell genetics with single-molecule localization microscopy and a palette of bespoke analytical tools, to visualize molecular transactions during RAD51 assembly in the cellular milieu at resolutions approaching 30-40 nm...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29306438/revealing-the-raft-domain-organization-in-the-plasma-membrane-by-single-molecule-imaging-of-fluorescent-ganglioside-analogs
#17
Kenichi G N Suzuki, Hiromune Ando, Naoko Komura, Miku Konishi, Akihiro Imamura, Hideharu Ishida, Makoto Kiso, Takahiro K Fujiwara, Akihiro Kusumi
Gangliosides have been implicated in a variety of physiological processes, particularly in the formation and function of raft domains in the plasma membrane. However, the scarcity of suitable fluorescent ganglioside analogs had long prevented us from determining exactly how gangliosides perform their functions in the live-cell plasma membrane. With the development of new fluorescent ganglioside analogs, as described by Komura et al. (2017), this barrier has been broken. We can now address the dynamic behaviors of gangliosides in the live-cell plasma membrane, using fluorescence microscopy, particularly by single-fluorescent molecule imaging and tracking...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29305173/direct-visualization-of-the-oligomeric-state-of-hemagglutinins-of-influenza-virus-by-high-resolution-atomic-force-microscopy
#18
Nikolay Barinov, Nikita Ivanov, Alexey Kopylov, Dmitry Klinov, Elena Zavyalova
High-resolution atomic force microscopy (AFM) is a powerful technique for the direct visualization of single molecules. Here, AFM is applied to characterize the oligomeric state of hemagglutinins of the influenza virus. Hemagglutinins are known to be present in a trimeric form inside the viral envelope. However, recombinant hemagglutinins are also present as large oligomers, which impair the functional activity of the protein. Five commercial recombinant hemagglutinins from the viral strains H1, H3, H5, H7, and H9 were studied with high-resolution AFM...
January 2, 2018: Biochimie
https://www.readbyqxmd.com/read/29303194/charge-transport-in-a-single-molecule-transistor-probed-by-scanning-tunneling-microscopy
#19
Samuel Bouvron, Romain Maurand, Alexander Graf, Philipp Erler, Luca Gragnaniello, Maxim Skripnik, Dirk Wiedmann, Clara Engesser, Cornelia Nef, Wangyang Fu, Christian Schönenberger, Fabian Pauly, Mikhail Fonin
We report on the scanning tunneling microscopy/spectroscopy (STM/STS) study of cobalt phthalocyanine (CoPc) molecules deposited onto a back-gated graphene device. We observe a clear gate voltage (Vg) dependence of the energy position of the features originating from the molecular states. Based on the analysis of the energy shifts of the molecular features upon tuning Vg, we are able to determine the nature of the electronic states that lead to a gapped differential conductance. Our measurements show that capacitive couplings of comparable strengths exist between the CoPc molecule and the STM tip as well as between CoPc and graphene, thus facilitating electronic transport involving only unoccupied molecular states for both tunneling bias polarities...
January 5, 2018: Nanoscale
https://www.readbyqxmd.com/read/29303192/water-induced-morphological-transformation-of-a-poly-aryl-ether-dendron-amphiphile-helical-fibers-to-nanorods-as-light-harvesting-antenna-systems
#20
Arunava Maity, Ananta Dey, Monalisa Gangopadhyay, Amitava Das
Self-assembly of suitable molecular building blocks is an efficient and convenient approach to generate nanomaterials with various morphologies and functions. Moreover, understanding the nature of molecules and controlling factors of their self-assembly process is crucial in fundamental aspects of molecular self-assembly which provide insights into the design of new assemblies with functional nano-architectures. To this end, the present study reports water induced self-assembled multifaceted morphology formation and the plausible pathway of the morphology transformation of a single poly(aryl ether) dendron amphiphile 1(D)...
January 5, 2018: Nanoscale
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