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Single molecule microscopy

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https://www.readbyqxmd.com/read/28731341/a-2d-coordination-network-that-detects-nitro-explosives-in-water-catalyzes-baylis-hillman-reactions-and-undergoes-unusual-2d%C3%A2-3d-single-crystal-to-single-crystal-transformation
#1
Vivekanand Sharma, Dinesh De, Sanchari Pal, Prithwidip Saha, Parimal K Bharadwaj
The solvothermal reaction of Zn(NO3)2·6H2O and a linear dicarboxylate ligand H2L, in the presence of urotropine in N,N'-dimethylformamide (DMF), gives rise to a new porous two-dimensional (2D) coordination network, {[Zn3(L)3(urotropine)2]·2DMF·3H2O}n (1), with hxl topology. Interestingly, framework 1 exhibits excellent emission properties owing to the presence of naphthalene moiety in the linker H2L, that can be efficiently suppressed by subtle quantity of nitro explosives in aqueous medium. Furthermore, presence of urotropine molecules bound to the metal centers, 1 is found to be an excellent heterogeneous catalyst meant for atom-economical C-C bond-forming Baylis-Hillman reactions...
July 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28731327/donor-acceptor-properties-of-a-single-molecule-altered-by-on-surface-complex-formation
#2
Tobias Meier, Rémy Pawlak, Shigeki Kawai, Yan Geng, Xunshan Liu, Silvio Decurtins, Prokop Hapala, Alexis Baratoff, Shi-Xia Liu, Pavel Jelinek, Ernst Meyer, Thilo Glatzel
Electron donor-acceptor molecules are of outstanding interest in molecular electronics and organic solar cells for their intramolecular charge transfer controlled via electrical or optical excitation. The preservation of their electronic character in the ground state upon adsorption on a surface is cardinal for their implementation in such single-molecule devices. Here, we investigate by atomic force microscopy and scanning tunneling microscopy a prototypical system consisting of a π-conjugated tetrathiafulvalene-fused dipyridophenazine molecule adsorbed on thin NaCl films on Cu(111)...
July 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/28726383/marangoni-convection-assisted-single-molecule-detection-with-nanojet-surface-enhanced-raman-spectroscopy
#3
Te-Wei Chang, Xinhao Wang, Amirreza Mahigir, Georgios Veronis, Gang Logan Liu, Manas Ranjan Gartia
Many single-molecule (SM) label-free techniques such as scanning probe microscopies (SPM) and magnetic force spectroscopies (MFS) provide high resolution surface topography information, but lack chemical information. Typical surface enhanced Raman spectroscopy (SERS) systems provide chemical information on the analytes, but lack spatial resolution. In addition, a challenge in SERS sensors is to bring analytes into the so-called "hot spots" (locations where the enhancement of electromagnetic field amplitude is larger than 10(3))...
July 20, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723958/can-single-molecule-localization-microscopy-be-used-to-map-closely-spaced-rgd-nanodomains
#4
Mahdie Mollazade, Thibault Tabarin, Philip R Nicovich, Alexander Soeriyadi, Daniel J Nieves, J Justin Gooding, Katharina Gaus
Cells sense and respond to nanoscale variations in the distribution of ligands to adhesion receptors. This makes single molecule localization microscopy (SMLM) an attractive tool to map the distribution of ligands on nanopatterned surfaces. We explore the use of SMLM spatial cluster analysis to detect nanodomains of the cell adhesion-stimulating tripeptide arginine-glycine-aspartic acid (RGD). These domains were formed by the phase separation of block copolymers with controllable spacing on the scale of tens of nanometers...
2017: PloS One
https://www.readbyqxmd.com/read/28723581/the-structure-and-function-of-cell-membranes-studied-by-atomic-force-microscopy
#5
REVIEW
Yan Shi, Mingjun Cai, Lulu Zhou, Hongda Wang
The cell membrane, involved in almost all communications of cells and surrounding matrix, is one of the most complicated components of cells. Lack of suitable methods for the detection of cell membranes in vivo has sparked debates on the biochemical composition and structure of cell membranes over half a century. The development of single molecule techniques, such as AFM, SMFS, and TREC, provides a versatile platform for imaging and manipulating cell membranes in biological relevant environments. Here, we discuss the latest developments in AFM and the progress made in cell membrane research...
July 16, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28723083/correction-to-observing-extremely-weak-protein-protein-interactions-with-conventional-single-molecule-fluorescence-microscopy
#6
Janghyun Yoo, Tae-Sun Lee, Byungsan Choi, Min Ju Shon, Tae-Young Yoon
No abstract text is available yet for this article.
July 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28718919/putting-rings-around-carbon-nanotubes
#7
Emilio M Pérez
In the last five years, we have developed synthetic methods towards encapsulation of single walled carbon nanotubes (SWNTs) into organic macrocycles, to form rotaxane-type molecules. These are the first examples of mechanically interlocked SWNTs derivatives (MINTs). In this article, I discuss our motivation to continue developing chemistry of SWNTs at a time well past their hype. We explain our synthetic strategy and characterization methodology in detail, stressing the general aspects. In particular, we emphasize the importance of adequate control experiments and bulk spectroscopic and analytical data to determine the structure of SWNT derivatives, as opposed to relying only (or mostly) on microscopy...
July 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28716648/applications-of-high-speed-atomic-force-microscopy-to-real-time-visualization-of-dynamic-biomolecular-processes
#8
REVIEW
Takayuki Uchihashi, Simon Scheuring
BACKGROUND: Many biological processes in a living cell are consequences of sequential and hierarchical dynamic events of biological macromolecules such as molecular interactions and conformational changes. Hence, knowledge of structures, assembly and dynamics of proteins is the foundation for understanding how biological molecules work. Among several techniques to analyze dynamics of proteins, high-speed atomic force microscopy (HS-AFM) is unique to provide direct information about both structure and dynamics of single proteins at work...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28714467/cryo-em-structures-of-the-atp-bound-vps4-e233q-hexamer-and-its-complex-with-vta1-at-near-atomic-resolution
#9
Shan Sun, Lin Li, Fan Yang, Xiaojing Wang, Fenghui Fan, Mengyi Yang, Chunlai Chen, Xueming Li, Hong-Wei Wang, Sen-Fang Sui
The cellular ESCRT-III (endosomal sorting complex required for transport-III) and Vps4 (vacuolar protein sorting 4) comprise a common machinery that mediates a variety of membrane remodelling events. Vps4 is essential for the machinery function by using the energy from ATP hydrolysis to disassemble the ESCRT-III polymer into individual proteins. Here, we report the structures of the ATP-bound Vps4(E233Q) hexamer and its complex with the cofactor Vta1 (vps twenty associated 1) at resolutions of 3.9 and 4.2 Å, respectively, determined by electron cryo-microscopy...
July 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28714316/through-a-window-brightly-a-review-of-selected-nanofabricated-thin-film-platforms-for-spectroscopy-imaging-and-detection
#10
Jason R Dwyer, Maher Harb
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing...
January 1, 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28712396/-response-surface-methodology-for-optimizing-the-technology-of-induction-and-isolation-of-dendritic-cells-by-multiple-cytokines
#11
Xunwei Duan, Guiqing Xiao, Yanlan Zhao, Lixing Wang, Chenna Zheng, Le Dong, Wenlin Wu
Objective To promote the induction and separation efficiency of bone marrow-derived dendritic cells (BMDCs) in vitro through optimizing the inducing and isolating process by multiple cytokines. Methods The factors to be optimized in single factor tests included recombinant mouse granulocyte macrophage-colony stimulating factor (rmGM-CSF), recombinant mouse interleukine 4 (rmIL-4), lipopolysaccharide (LPS), recombinant mouse tumor necrosis factor α (rmTNF-α) and inducing time. The numbers of immature dendritic cells (imDCs) and mature dendritic cells (mDCs) were investigated as the indicators...
July 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28712296/competing-annulene-and-radialene-structures-in-a-single-anti-aromatic-molecule-studied-by-high-resolution-atomic-force-microscopy
#12
Shigeki Kawai, Keisuke Takahashi, Shingo Ito, Rémy Pawlak, Tobias Meier, Peter Spijker, Filippo Federici Canova, John Tracey, Kyoko Nozaki, Adam S Foster, Ernst Meyer
According to Hückel theory, an anti-aromatic molecule possessing (4n)π-electrons becomes unstable. Although the stabilization has been demonstrated by radialene-type structures-fusing aromatic rings to anti-aromatic rings-in solution, such molecules have never been studied at a single molecular level. Here, we synthesize a cyclobutadiene derivative, dibenzo[b,h]biphenylene, by an on-surface intramolecular reaction. With a combination of high-resolution atomic force microscopy and density functional theory calculations, we found that a radialene structure significantly reduces the anti-aromaticity of the cyclobutadiene core, extracting π-electrons, while the small four-membered cyclic structure keeps a high density of the total charge...
July 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28711172/the-effect-of-rna-secondary-structure-on%C3%A2-the%C3%A2-self-assembly-of-viral-capsids
#13
Christian Beren, Lisa L Dreesens, Katherine N Liu, Charles M Knobler, William M Gelbart
Previous work has shown that purified capsid protein (CP) of cowpea chlorotic mottle virus (CCMV) is capable of packaging both purified single-stranded RNA molecules of normal composition (comparable numbers of A, U, G, and C nucleobases) and of varying length and sequence, and anionic synthetic polymers such as polystyrene sulfonate. We find that CCMV CP is also capable of packaging polyU RNAs, which-unlike normal-composition RNAs-do not form secondary structures and which act as essentially structureless linear polymers...
July 12, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28708098/combining-primed-photoconversion-and-uv-photoactivation-for-aberration-free-live-cell-compliant-multi-color-single-molecule-localization-microscopy-imaging
#14
David Virant, Bartosz Turkowyd, Alexander Balinovic, Ulrike Endesfelder
Super-resolution fluorescence microscopy plays a major role in revealing the organization and dynamics of living cells. Nevertheless, single-molecule localization microscopy imaging of multiple targets is still limited by the availability of suitable fluorophore combinations. Here, we introduce a novel imaging strategy which combines primed photoconversion (PC) and UV-photoactivation for imaging different molecular species tagged by suitable fluorescent protein combinations. In this approach, the fluorescent proteins can be specifically photoactivated/-converted by different light wavelengths using PC and UV-activation modes but emit fluorescence in the same spectral emission channel...
July 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28707196/reversible-association-of-the-hemagglutinin-subcomplex-ha-33-ha-17-trimer-with-the-botulinum-toxin-complex
#15
Yoshimasa Sagane, Shingo Mutoh, Ryosuke Koizumi, Tomonori Suzuki, Shin-Ichiro Miyashita, Keita Miyata, Tohru Ohyama, Koichi Niwa, Toshihiro Watanabe
Botulinum neurotoxin (BoNT) associates with nontoxic proteins, either a nontoxic nonhemagglutinin (NTNHA) or the complex of NTNHA and hemagglutinin (HA), to form M- or L-toxin complexes (TCs). Single BoNT and NTNHA molecules are associated and form M-TC. A trimer of the 70-kDa HA protein (HA-70) attaches to the M-TC to form M-TC/HA-70. Further, 1-3 arm-like 33- and 17-kDa HA molecules (HA-33/HA-17 trimer), consisting of 1 HA-17 protein and 2 HA-33 proteins, can attach to the M-TC/HA-70 complex, yielding 1-, 2-, and 3-arm L-TC...
July 13, 2017: Protein Journal
https://www.readbyqxmd.com/read/28706306/ligand-induced-type-ii-interleukin-4-receptor-dimers-are-sustained-by-rapid-re-association-within-plasma-membrane-microcompartments
#16
David Richter, Ignacio Moraga, Hauke Winkelmann, Oliver Birkholz, Stephan Wilmes, Markos Schulte, Michael Kraich, Hella Kenneweg, Oliver Beutel, Philipp Selenschik, Dirk Paterok, Martynas Gavutis, Thomas Schmidt, K Christopher Garcia, Thomas D Müller, Jacob Piehler
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand-receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization...
July 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28703339/the-synthesis-and-photophysical-analysis-of-a-series-of-4-nitrobenzochalcogenadiazoles-for-super-resolution-microscopy
#17
Daniel Ray Jenkinson, Ashley Cadby, Simon Jones
A series of 4-nitrobenzodiazoles with atomic substitution through the chalcogen group were synthesised and their photophysical properties analysed with a view for use in single-molecule localisation microscopy. Sub-diffraction resolution imaging was achieved for silica nanoparticles coated with each dye. Those containing larger atoms were favoured for super-resolution microscopy due to a reduced blink rate (required for stochastic events to be localised). The sulfur containing molecule was deemed most amenable for widespread use due to the ease of synthetic manipulation compared to the selenium containing derivative...
July 13, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28701712/use-of-single-frequency-impedance-spectroscopy-to-characterize-the-growth-dynamics-of-biofilm-formation-in-pseudomonas-aeruginosa
#18
Jozef B J H van Duuren, Mathias Müsken, Bianka Karge, Jürgen Tomasch, Christoph Wittmann, Susanne Häussler, Mark Brönstrup
Impedance spectroscopy has been applied in prokaryotic and eukaryotic cytometry as a label-free method for the investigation of adherent cells. In this paper, its use for characterizing the growth dynamics of P. aeruginosa biofilms is described and compared to crystal violet staining and confocal microscopy. The method allows monitoring the growth of biofilm-forming P. aeruginosa in a continuous and label-free manner over a period of 72 h in a 96 well plate format. Impedance curves obtained for P. aeruginosa PA14 wild type and mutant strains with a transposon insertion in pqsA and pelA genes exhibited distinct phases...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698239/enzymatic-production-of-single-molecule-fish-and-rna-capture-probes
#19
Imre Gaspar, Frank Wippich, Anne Ephrussi
Arrays of singly-labelled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single molecule microscopy analysis and high efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that 1) all steps of the oligonucleotide labelling - including conjugation, enzymatic synthesis and product purification - can be performed in a standard biology laboratory, 2) the process yields >90 %, often >95 % labeled product with minimal carry-over of impurities and 3) the oligonucleotides can be labeled with different dyes or biotin, allowing single molecule FISH or RNA affinity purification, and northern-blot analysis to be performed...
July 11, 2017: RNA
https://www.readbyqxmd.com/read/28694765/cellular-uptake-and-anti-tumor-activity-of-gemcitabine-conjugated-with-new-amphiphilic-cell-penetrating-peptides
#20
Parvin Zakeri-Milani, Samad Mussa Farkhani, Ali Shirani, Samaneh Mohammadi, Javid Shahbazi Mojarrad, Jafar Akbari, Hadi Valizadeh
Gemcitabine (Gem) is used as a single agent or in combination with other anticancer agents to treat many types of solid tumors. However, it has many limitations such as a short plasma half-life, dose-limiting toxicities and drug resistance. Cell-penetrating peptides (CPPs) are short peptides which may deliver a large variety of cargo molecules into the cancerous cells. The current study was designed to evaluate the antiproliferative activity of gemcitabine chemically conjugated to CPPs. The peptides were synthesized using solid phase synthesis procedure...
2017: EXCLI journal
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