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Yin-Shan Meng, Shang-Da Jiang, Bing-Wu Wang, Song Gao
Single-molecule magnets (SMMs) can retain their magnetization status preferentially after removal of the magnetic field below a certain temperature. The unique property, magnetic bistable status, enables the molecule-scale SMM to become the next-generation high-density information storage medium. SMMs' new applications are also involved in high-speed quantum computation and molecular spintronics. The development of coordination chemistry, especially in transition metal (3d) and lanthanide (4f) complexes, diversifies SMMs by introducing new ones...
October 21, 2016: Accounts of Chemical Research
Philipp Leinen, Matthew F B Green, Taner Esat, Christian Wagner, F Stefan Tautz, Ruslan Temirov
Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building blocks in a bottom-up approach is still open. The scanning probe microscope (SPM) could be a tool of choice; however, SPM-based manipulation was until recently limited to two dimensions (2D). Binding the SPM tip to a molecule at a well-defined position opens an opportunity of controlled manipulation in 3D space. Unfortunately, 3D manipulation is largely incompatible with the typical 2D-paradigm of viewing and generating SPM data on a computer...
October 2, 2016: Journal of Visualized Experiments: JoVE
Satoshi Habuchi, Takuya Yamamoto, Yasuyuki Tezuka
We demonstrate a method for the synthesis of cyclic polymers and a protocol for characterizing their diffusive motion in a melt state at the single molecule level. An electrostatic self-assembly and covalent fixation (ESA-CF) process is used for the synthesis of the cyclic poly(tetrahydrofuran) (poly(THF)). The diffusive motion of individual cyclic polymer chains in a melt state is visualized using single molecule fluorescence imaging by incorporating a fluorophore unit in the cyclic chains. The diffusive motion of the chains is quantitatively characterized by means of a combination of mean-squared displacement (MSD) analysis and a cumulative distribution function (CDF) analysis...
September 26, 2016: Journal of Visualized Experiments: JoVE
Gil Henkin, Daniel Berard, Francis Stabile, Marjan Shayegan, Jason S Leith, Sabrina R Leslie
We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends Convex Lens-induced Confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in-situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array...
October 21, 2016: Analytical Chemistry
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single molecule molecular inversion probe (smMIP)-based targeted next generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
Gang Li, Mengyu Shen, Shuai Le, Yinling Tan, Ming Li, Xia Zhao, Wei Shen, Yuhui Yang, Jing Wang, Hongbin Zhu, Shu Li, Xiancai Rao, Fuquan Hu, Shuguang Lu
As a third-generation sequencing method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for re-sequencing projects and de novo assembly. In this study, Pseudomonas aeruginosa PA1 was characterized and re-sequenced using SMRT technology. PA1 was also subjected to genomic, comparative, and pan-genomic analyses. The multi-drug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins, secretion system proteins, type II toxin-antitoxin pairs, and genomic islands...
October 20, 2016: Bioscience Reports
N V Klementieva, K A Lukyanov, N M Markina, S A Lukyanov, E V Zagaynova, A S Mishin
Recently, an unusual phenomenon of primed conversion of fluorescent protein Dendra2 by combined action of blue (488 nm) and near-infrared (700-780 nm) lasers was discovered. Here we demonstrate that primed conversion can be induced by red lasers (630-650 nm) common for most confocal and single molecule detection microscopes.
October 20, 2016: Chemical Communications: Chem Comm
Jinglin Fu, Yuhe Renee Yang, Soma Dhakal, Zhao Zhao, Minghui Liu, Ting Zhang, Nils G Walter, Hao Yan
In nature, the catalytic efficiency of multienzyme complexes highly depends on their spatial organization. The positions and orientations of the composite enzymes are often precisely controlled to facilitate substrate transport between them. Self-assembled DNA nanostructures hold great promise for organizing biomolecules at the nanoscale. Here, we present detailed protocols for exploiting DNA nanostructures as assembly scaffolds that organize the spatial arrangements of multienzyme cascades with control over their relative distance, compartmentalization and substrate diffusion paths...
November 2016: Nature Protocols
Debojit Bhattacharya, Suranjan Shil, Anirban Misra, Laimutis Bytautas, Douglas J Klein
Here we study a set of novel magnetic organic molecular species with different halide ions (fluoride, chloride, bromide) absorbed ~2Å above or below the center of an aromatic π-ring in an m-aminyl diradical. Focus is on the nature of anion-π interaction and its impact on magnetic properties, specifically on magnetic anisotropy and on intramolecular magnetic exchange coupling. In the development of single molecule magnets, magnetic anisotropy is considered to be the most influential factor. A new insight regarding the magnetic anisotropy which determines the barrier height for relaxation of magnetization of m-aminyl diradical-derived anionic complexes is obtained from calculations of the axial Zero-Field-Splitting (ZFS) parameter D...
October 20, 2016: Journal of Physical Chemistry. A
Chao-Chen Lin, Hsin-Fang Hsu, Peter Jomo Walla
The fusion of two opposing membranes is essential in biological functions such as fertilization, viral entry, membrane trafficking and synaptic transmission. Before the membrane bilayers are fully connected, at some stage a hemifusion intermediate-when the outer leaflets are merged but not the inner leaflets-is formed. However, the position of hemifusion in the energy landscape and the duration of it vary and have not been fully mapped out. To date, there has not been a way to differentiate lipid mixing of the two leaflets directly in a single experiment...
October 20, 2016: Journal of Physical Chemistry. B
David A Selck, Rustem F Ismagilov
Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification...
2016: PloS One
Lei Zhang, Theresa Chimamkpam, Camelia I Onet, Nianyong Zhu, Rodolphe Clérac, Wolfgang Schmitt
We report a supramolecular approach to mixed-valent Mn coordination clusters that demonstrates how halide ions can be applied to influence the assembly of distinct tetranuclear building units to produce a number of related Mn coordination clusters with dense core structures that derive from a cuboctahedral arrangement of Mn ions. In all compounds the alignment of the Jahn-Teller axes of the Mn(III) centers coincides with the positions of the stabilizing chloride ligands. Thus, the relative chloride concentrations in the reaction mixtures allow us to modify the symmetry and magnetic anisotropy of this basic core structures resulting in isotropic polynuclear high-spin complexes at high Cl(-) concentrations and Single-Molecule Magnets at lower relative Cl(-) concentrations...
October 19, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Janghyun Yoo, Tae-Sun Lee, Byungsan Choi, Min Ju Shon, Tae-Young Yoon
Extremely weak protein-protein interactions (PPIs), signified by micromolar or even millimolar dissociation constants, are one of the keys to understanding the rapid responses of cellular systems. Although single-molecule methods are particularly useful in determining kinetics of biological processes, their application is largely limited to rather strong interactions because of the diffraction-limited observation volume. In this study, we report a single-molecule method that allows the characterization of PPIs using a prey concentration four orders of magnitude lower than the dissociation constant...
October 19, 2016: Journal of the American Chemical Society
Masaaki Mitsui, Koji Higashi, Yohei Hirumi, Kenji Kobayashi
The effects of supramolecular encapsulation on the photophysics and photostability of a highly fluorescent dimeric derivative of 2,6-diacetoxy-9,10-bis(arylethynyl)anthracene (G2) were investigated by single-molecule fluorescence spectroscopy (SMFS). The fluorescence properties of free-G2 and its self-assembled boronic ester encapsulation complex, G2@(Cap)2, were compared in solution and a glassy polymer film. The fluorescence spectral characteristics and theoretical calculations suggest that the environment affects the excited-state conformation and subsequent fluorescence emission of G2@(Cap)2...
October 18, 2016: Journal of Physical Chemistry. A
Subarna Dutta, Maitree Bhattacharyya, Kaushik Sengupta
Lamins are mechanosensitive and elastic components of the nuclear lamina that respond to external mechanical cues by altering gene regulation in a feedback mechanism. Numerous mutations in A-type lamins cause a plethora of diverse diseases collectively termed as laminopathies, the majority of which are characterized by irregularly shaped, fragile, and plastic nuclei. These nuclei are challenged to normal mechanotransduction and lead to disease phenotypes. Here, we review our current understanding of the nucleocytoskeleton coupling in mechanotransduction mediated by lamins...
October 14, 2016: Cells
Albert C Aragonès, Ernesto Medina, Miriam Ferrer-Huerta, Nuria Gimeno, Meritxell Teixidó, Julio L Palma, Nongjian Tao, Jesus M Ugalde, Ernest Giralt, Ismael Díez-Pérez, Vladimiro Mujica
The electronic spin filtering capability of a single chiral helical peptide is measured. A ferromagnetic electrode source is employed to inject spin-polarized electrons in an asymmetric single-molecule junction bridging an α-helical peptide sequence of known chirality. The conductance comparison between both isomers allows the direct determination of the polarization power of an individual chiral molecule.
October 18, 2016: Small
Alexey L Chernobrovkin, Roman A Zubarev
While the focus of attempts to classify cell death programs has finally shifted in 2010s from microscopy-based morphological characteristics to biochemical assays, more recent discoveries have put the underlying assumptions of many such assays under severe stress, mostly because of the limited specificity of the assays. On the other hand, proteomics can quantitatively measure the abundances of thousands of proteins in a single experiment. Thus proteomics could develop a modern alternative to both semiquantitative morphology assessment as well as single-molecule biochemical assays...
2016: Cell Death Discovery
Carmine Di Rienzo, Paolo Annibale
The determination of the mode and rapidity of motion of individual molecules within a biological sample is becoming a more and more common analysis in biophysical investigations. Single molecule tracking (SMT) techniques allow reconstructing the trajectories of individual molecules within a movie, provided that the position from one frame to the other can be correctly linked. The outcomes, however, appear to depend on the specific method used, and most techniques display a limitation to capture fast modes of motion in a crowded environment...
October 1, 2016: Optics Letters
Christine Koehler, Paul F Sauter, Mirella Wawryszyn, Gemma Estrada Girona, Kapil Gupta, Jonathan J M Landry, Markus Hsi-Yang Fritz, Ksenija Radic, Jan-Erik Hoffmann, Zhuo A Chen, Juan Zou, Piau Siong Tan, Bence Galik, Sini Junttila, Peggy Stolt-Bergner, Giancarlo Pruneri, Attila Gyenesei, Carsten Schultz, Moritz Bosse Biskup, Hueseyin Besir, Vladimir Benes, Juri Rappsilber, Martin Jechlinger, Jan O Korbel, Imre Berger, Stefan Braese, Edward A Lemke
We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, 'MultiBacTAG', (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure-function studies of novel eukaryotic complexes using single-molecule Förster resonance energy transfer as well as site-specific crosslinking strategies...
October 17, 2016: Nature Methods
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R Ecker, Dario Cantu, David R Rank, Michael C Schatz
While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms ( to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv...
October 17, 2016: Nature Methods
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