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Single molecule localization

Indrajyoti Indra, Jongho Choi, Chi-Shuo Chen, Regina B Troyanovsky, Lawrence Shapiro, Barry Honig, Sergey M Troyanovsky
Adherens junctions (AJs) play a fundamental role in tissue integrity; however, the organization and dynamics of the key AJ transmembrane protein, E-cadherin, both inside and outside of AJs, remain controversial. Here we have studied the distribution and motility of E-cadherin in punctate AJs (pAJs) of A431 cells. Using single-molecule localization microscopy, we show that pAJs in these cells reach more than 1 μm in length and consist of several cadherin clusters with crystal-like density interspersed within sparser cadherin regions...
April 24, 2018: Proceedings of the National Academy of Sciences of the United States of America
Francesca Ruggeri, Madhavi Krishnan
We demonstrate the ability to confine a single molecule in solution by spatial modulation of its local configurational entropy. Previously we established electrostatic trapping of a charged macromolecule by geometric tailoring of a repulsive electrical interaction potential in a parallel plate system. However, since the lifetime of the trapped state depends exponentially on the electrical charge of the molecule, the electrostatic interaction alone is often insufficient in magnitude to stably confine molecules carrying a net charge of magnitude <5 e...
April 24, 2018: Nano Letters
Xiaoli Wang, Longqing Yang, LvZhou Ye, Xiao Zheng, YiJing Yan
The precise tuning of local spin states in adsorbed organometallic molecules by a mechanically controlled scanning tunneling microscope (STM) tip has become a focus of recent experiments. However, the underlying mechanisms remain somewhat unclear. We investigate theoretically the STM-tip control of local spin states in a single iron(II) porphyrin molecule adsorbed on the Pb(111) substrate. A combined density functional theory and hierarchical equations of motion approach is employed to simulate the tip tuning process, in conjunction with the complete active space self-consistent field method for an accurate computation of magnetic anisotropy...
April 24, 2018: Journal of Physical Chemistry Letters
Anna-Karin Gustavsson, Petar N Petrov, Maurice Y Lee, Yoav Shechtman, W E Moerner
To obtain a complete picture of subcellular nanostructures, cells must be imaged with high resolution in all three dimensions (3D). Here, we present tilted light sheet microscopy with 3D point spread functions (TILT3D), an imaging platform that combines a novel, tilted light sheet illumination strategy with engineered 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. TILT3D is built upon a standard inverted microscope and has minimal custom parts...
February 2018: Proceedings of SPIE
Michael D Tomasini, Daniel S Johnson, Joshua S Mincer, Sanford M Simon
We report a computational model for the assembly of HIV-1 Gag into immature viral particles at the plasma membrane. To reproduce experimental structural and kinetic properties of assembly, a process occurring on the order of minutes, a coarse-grained representation consisting of a single particle per Gag molecule is developed. The model uses information relating the functional interfaces implicated in Gag assembly, results from cryo electron-tomography, and biophysical measurements from fluorescence microscopy, such as the dynamics of Gag assembly at single virions...
2018: PloS One
Silvia Colabrese, Marco Castello, Giuseppe Vicidomini, Alessio Del Bue
Single molecule localisation (SML) microscopy is a fundamental tool for biological discoveries; it provides sub-diffraction spatial resolution images by detecting and localizing "all" the fluorescent molecules labeling the structure of interest. For this reason, the effective resolution of SML microscopy strictly depends on the algorithm used to detect and localize the single molecules from the series of microscopy frames. To adapt to the different imaging conditions that can occur in a SML experiment, all current localisation algorithms request, from the microscopy users, the choice of different parameters...
April 1, 2018: Biomedical Optics Express
Bijin Li, Linsen Zhou, Hu Cheng, Quan Huang, Jingbo Lan, Liang Zhou, Jingsong You
The photoluminescence (PL) and electroluminescence (EL) properties of two highly efficient excited state intramolecular proton transfer (ESIPT) molecules, 2-(2'-hydroxyphenyl)oxazoles containing one triphenylamine (TPA) ( 1 ) and two TPAs ( 2 ) respectively, are studied systematically. The enol-forms of both 1 and 2 possess highly hybridized local and charge transfer (HLCT) excited state character, while their excited-state keto-forms are not of obvious HLCT character. A 1 -based device exhibits green-white electroluminescence with Commission Internationale d'Eclairage (CIE) coordinates of (0...
February 7, 2018: Chemical Science
Le Wang, Shenfei Zong, Zhuyuan Wang, Ju Lu, Chen Chen, Ruohu Zhang, Yiping Cui
Single molecule localization microscopy (SMLM) is a powerful tool for imaging biological targets at the nanoscale. In this report, we present SMLM imaging of telomeres and centromeres using fluorescence in situ hybridization (FISH). The FISH probes were fabricated by decorating CdSSe/ZnS quantum dots (QDs) with telomere or centromere complementary DNA strands. SMLM imaging experiments using commercially available peptide nucleic acid (PNA) probes labeled with organic fluorophores were also conducted to demonstrate the advantages of using QDs FISH probes...
April 19, 2018: Nanotechnology
Zahra Khatti, Seyed Majid Hashemianzadeh, Seyed Ali Shafiei
Purpose: Drug delivery has a critical role in the treatment of cancer, in particular, carbon nanotubes for their potential use in various biomedical devices and therapies. From many other materials which could be more biocompatible and biodegradable and which could form single-walled nanotubes, silicon carbide was selected. Methods: To compare two drug delivery systems based on single-walled nanotubes, molecular dynamic simulations were applied and encapsulation behavior of the drug carboplatin was investigated inside the silicon carbide nanotube and the carbon nanotube...
March 2018: Advanced Pharmaceutical Bulletin
Oliver Birkholz, Jonathan R Burns, Christian P Richter, Olympia E Psathaki, Stefan Howorka, Jacob Piehler
Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes...
April 18, 2018: Nature Communications
Christiaan Nick Hulleman, Weixing Li, Ingo Gregor, Bernd Rieger, Jörg Enderlein
Single Molecule Localization Microscopy has become one of the most successful and widely applied methods of Super-resolution Fluorescence Microscopy. Its achievable resolution strongly depends on the number of detectable photons from a single molecule until photobleaching. By cooling a sample from room temperature down to liquid nitrogen tempe- ratures, the photostability of dyes can be enhanced by more than 100 fold, which results in an improvement in localization precision greater than 10 times. Here, we investigate a variety of fluorescent dyes in the red spectral region, and we find an average photon yield between 3...
April 16, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Pablo Ares, Pilar Amo-Ochoa, José M Soler, Juan José Palacios, Julio Gómez-Herrero, Félix Zamora
Molecular wires are essential components for future nanoscale electronics. However, the preparation of individual long conductive molecules is still a challenge. MMX metal-organic polymers are quasi-1D sequences of single halide atoms (X) bridging subunits with two metal ions (MM) connected by organic ligands. They are excellent electrical conductors as bulk macroscopic crystals and as nanoribbons. However, according to theoretical calculations, the electrical conductance found in the experiments should be even higher...
April 16, 2018: Advanced Materials
Wei Ouyang, Andrey Aristov, Mickaël Lelek, Xian Hao, Christophe Zimmer
The speed of super-resolution microscopy methods based on single-molecule localization, for example, PALM and STORM, is limited by the need to record many thousands of frames with a small number of observed molecules in each. Here, we present ANNA-PALM, a computational strategy that uses artificial neural networks to reconstruct super-resolution views from sparse, rapidly acquired localization images and/or widefield images. Simulations and experimental imaging of microtubules, nuclear pores, and mitochondria show that high-quality, super-resolution images can be reconstructed from up to two orders of magnitude fewer frames than usually needed, without compromising spatial resolution...
April 16, 2018: Nature Biotechnology
Laura Avogaro, Emmanuelle Querido, Myriam Dalachi, Michael F Jantsch, Pascal Chartrand, Emilio Cusanelli
Telomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres...
April 16, 2018: RNA Biology
Eric H Kim, Gregory Chin, Guoxin Rong, Kira E Poskanzer, Heather A Clark
Fluorescent nanosensors and molecular probes are next-generation tools for imaging chemical signaling inside and between cells. Electrophysiology has long been considered the gold standard in elucidating neural dynamics with high temporal resolution and precision, particularly on the single-cell level. However, electrode-based techniques face challenges in illuminating the specific chemicals involved in neural cell activation with adequate spatial information. Measuring chemical dynamics is of fundamental importance to better understand synergistic interactions between neurons as well as interactions between neurons and non-neuronal cells...
April 13, 2018: Accounts of Chemical Research
Yu-Wen Su, Wei Wang
Surface plasmon resonance (SPR) has become a well-recognized label-free technique for measuring the binding kinetics between biomolecules since the invention of the first SPR-based immunosensor in 1980s. The most popular and traditional format for SPR analysis is to monitor the real-time optical signals when a solution containing ligand molecules is flowing over a sensor substrate functionalized with purified receptor molecules. In recent years, rapid development of several kinds of SPR imaging techniques have allowed for mapping the dynamic distribution of local mass density within single living cells with high spatial and temporal resolutions and reliable sensitivity...
April 12, 2018: Analytical and Bioanalytical Chemistry
Reut Ben-Menachem, Katherine Wang, Orly Marcu, Zhang Yu, Teck Kwang Lim, Qingsong Lin, Ora Schueler-Furman, Ophry Pines
Molecules of single proteins, echoforms, can be distributed between two (or more) subcellular locations, a phenomenon which we refer to as dual targeting or dual localization. The yeast aconitase gene ACO1 (778 amino acids), encodes a single translation product that is nonetheless dual localized to the cytosol and mitochondria by a reverse translocation mechanism. The solved crystal structure of aconitase isolated from porcine heart mitochondria shows that it has four domains. The first three tightly associated N-terminal domains are tethered to the larger C-terminal fourth domain (C-terminal amino acids 517-778)...
April 12, 2018: Scientific Reports
Angelika Balliou, Mirtat Bouroushian, Antonios M Douvas, George Skoulatakis, Stella Kennou, Nikos Glezos
All-inorganic self-arranged molecular transition metal oxide hyperstructures based on polyoxometalate molecules (POMs) are fabricated and tested as electronically tunable components in emerging electronic devices. POM hyperstructures reveal great potential as charging nodes of tunable charging level for molecular memories and as enhancers of interfacial electron/hole injection for photovoltaic stacks. STM, UPS, UV-Vis spectroscopy and AFM measurements show that this functionality stems from the films' ability to structurally tune their HOMO-LUMO levels and electron localization length at room temperature...
April 12, 2018: Nanotechnology
Yiming Li, Markus Mund, Philipp Hoess, Joran Deschamps, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries
We present a real-time fitter for 3D single-molecule localization microscopy using experimental point spread functions (PSFs) that achieves minimal uncertainty in 3D on any microscope and is compatible with any PSF engineering approach. We used this method to image cellular structures and attained unprecedented image quality for astigmatic PSFs. The fitter compensates for most optical aberrations and makes accurate 3D super-resolution microscopy broadly accessible, even on standard microscopes without dedicated 3D optics...
April 9, 2018: Nature Methods
Marius S Frank, Christof Hättig
We present a pair natural orbital (PNO)-based implementation of coupled cluster singles and doubles (CCSD) excitation energies that builds upon the previously proposed state-specific PNO approach to the excited state eigenvalue problem. We construct the excited state PNOs for each state separately in a truncated orbital specific virtual basis and use a local density-fitting approximation to achieve an at most quadratic scaling of the computational costs for the PNO construction. The earlier reported excited state PNO construction is generalized such that a smooth convergence of the results for charge transfer states is ensured for general coupled cluster methods...
April 7, 2018: Journal of Chemical Physics
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