keyword
MENU ▼
Read by QxMD icon Read
search

single-molecule

keyword
https://www.readbyqxmd.com/read/28107006/facilitated-diffusion-of-transcription-factor-proteins-with-anomalous-bulk-diffusion
#1
Lin Liu, Andrey G Cherstvy, Ralf Metzler
What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28104618/hysa-a-hybrid-structural-variant-assembly-approach-using-next-generation-and-single-molecule-sequencing-technologies
#2
Xian Fan, Mark Chaisson, Luay Nakhleh, Ken Chen
Achieving complete, accurate and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a hybrid structural variant assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variations in human genomes...
January 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28104452/cystoviral-rna-directed-rna-polymerases-regulation-of-rna-synthesis-on-multiple-time-and-length-scales
#3
REVIEW
Sébastien Alphonse, Ranajeet Ghose
P2, an RNA-directed RNA polymerase (RdRP), is encoded on the largest of the three segments of the double-stranded RNA genome of cystoviruses. P2 performs the dual tasks of replication and transcription de novo on single-stranded RNA templates, and plays a critical role in the viral life-cycle. Work over the last few decades has yielded a wealth of biochemical and structural information on the functional regulation of P2, on its role in the spatiotemporal regulation of RNA synthesis and its variability across the Cystoviridae family...
January 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28103588/quantifying-kinetics-from-time-series-of-single-molecule-fret-efficiency-histograms
#4
Stephan Benke, Daniel Nettels, Hagen Hofmann, Benjamin Schuler
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, F��rster resonance energy transfer (FRET) in combination with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data...
January 19, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28102201/direct-pip2-binding-mediates-stable-oligomer-formation-of-the-serotonin-transporter
#5
Andreas Anderluh, Tina Hofmaier, Enrico Klotzsch, Oliver Kudlacek, Thomas Stockner, Harald H Sitte, Gerhard J Schütz
The human serotonin transporter (hSERT) mediates uptake of serotonin from the synaptic cleft and thereby terminates serotonergic signalling. We have previously found by single-molecule microscopy that SERT forms stable higher-order oligomers of differing stoichiometry at the plasma membrane of living cells. Here, we report that SERT oligomer assembly at the endoplasmic reticulum (ER) membrane follows a dynamic equilibration process, characterized by rapid exchange of subunits between different oligomers, and by a concentration dependence of the degree of oligomerization...
January 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28100105/inventing-a-co-axial-atomic-resolution-patch-clamp-to-study-a-single-resonating-protein-complex-and-ultra-low-power-communication-deep-inside-a-living-neuron-cell
#6
Subrata Ghosh, Satyajit Sahu, Lokesh Agrawal, Takashi Shiga, Anirban Bandyopadhyay
To read the signals of single molecules in vitro on a surface, or inside a living cell or organ, we introduce a coaxial atom tip (coat) and a coaxial atomic patch clamp (COAPAP). The metal-insulator-metal cavity of these probes extends to the atomic scale (0.1[Formula: see text]nm), it eliminates the cellular or environmental noise with a S/N ratio 10(5). Five ac signals are simultaneously applied during a measurement by COAT and COAPAP to shield a true signal under environmental noise in five unique ways. The electromagnetic drive in the triaxial atomic tips is specifically designed to sense anharmonic vibrational and transmission signals for any systems between 0...
January 18, 2017: Journal of Integrative Neuroscience
https://www.readbyqxmd.com/read/28099797/epitaxy-induced-assembly-and-enantiomeric-switching-of-an-on-surface-formed-dinuclear-organocobalt-complex
#7
Raphael Hellwig, Tobias Paintner, Zhi Chen, Mario Ruben, Ari P Seitsonen, Florian Klappenberger, Harald Brune, Johannes V Barth
We report on the surface-guided synthesis of an unprecedented dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultra-high vacuum conditions onto Ag(111). After Co dosage at 200 Kelvin, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed host-guest complexes...
January 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28098976/adsorption-neutralization-model-and-floc-growth-kinetics-properties-of-aluminum-coagulants-based-on-sips-and-boltzmann-equation
#8
Zhen Wu, Xian Zhang, Chunjiao Zhou, Jing-Lin Pang, Panyue P Zhang
Single-molecule aluminum salt AlCl3, medium polymerized polyaluminium chloride (PAC) and high polymerized polyaluminium chloride (HPAC) were prepared in laboratory. The characteristics and coagulation properties of these prepared aluminum salts were investigated. The Langmuir, Freundlich and Sips adsorption isotherms were firstly used to describe the adsorption neutralization process in coagulation, and the Boltzmann equation was used to fit the reaction kinetics of floc growth in flocculation. It was novel to find that the experimental data fitted well with the Sips and Boltzmann equation, and the significance of parameters in the equations was discussed simultaneously...
January 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28098445/circular-and-chainlike-copper-ii-lanthanide-iii-complexes-generated-by-assembly-reactions-of-racemic-and-chiral-copper-ii-cross-linking-ligand-complexes-with-ln-iii-no3-3%C3%A2-6h2o-ln-iii-gd-iii-tb-iii-dy-iii
#9
Takahiro Ueno, Takeshi Fujinami, Naohide Matsumoto, Masaki Furusawa, Ryo Irie, Nazzareno Re, Takuya Kanetomo, Takayuki Ishida, Yukinari Sunatsuki
The 1:1 assembly reaction of the racemic form of the cross-linking ligand complex Na[Cu(II)L(dpen(1R2R/1S2S))] with Ln(III)(NO3)3·6H2O gave the centrosymmetric circular (Cu(II)Ln(III))2 complex [Cu(II)L(dpen(1R2R/1S2S))Ln(III)(NO3)2]2 (1Ln: Ln = Gd, Tb, Dy), while the reaction of the enantiopure form Na[Cu(II)L(dpen(1R2R))] with Ln(III)(NO3)3·6H2O gave the chiral chainlike (Cu(II)Ln(III))1∞ complex [Cu(II)L(dpen(1R2R))Ln(III)(NO3)2(CH3CN)]1∞·CH3CN (2Ln: Ln = Gd, Tb, Dy), where {Cu(II)L(dpen(1R2R))}(-) is (N-((1R,2R)-2-(((E)-3-ethoxy-2-oxybenzylidene)amino)-1,2-diphenylethyl)-2-oxybenzamide)copper(II) and {Cu(II)L(dpen(1R2R/1S2S))}(-) is the racemic mixture of {Cu(II)L(dpen(1R2R))}(-) and {Cu(II)L(dpen(1S2S))}(-)...
January 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28098202/superresolution-imaging-of-clinical-formalin-fixed-paraffin-embedded-breast-cancer-with-single-molecule-localization-microscopy
#10
Matthew K Creech, Jing Wang, Xiaolin Nan, Summer L Gibbs
Millions of archived formalin-fixed, paraffin-embedded (FFPE) specimens contain valuable molecular insight into healthy and diseased states persevered in their native ultrastructure. To diagnose and treat diseases in tissue on the nanoscopic scale, pathology traditionally employs electron microscopy (EM), but this platform has significant limitations including cost and painstaking sample preparation. The invention of single molecule localization microscopy (SMLM) optically overcame the diffraction limit of light to resolve fluorescently labeled molecules on the nanoscale, leading to many exciting biological discoveries...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096444/single-molecule-fret-rosetta-reveals-rna-structural-rearrangements-during-human-telomerase-catalysis
#11
Joseph W Parks, Kalli Kappel, Rhiju Das, Michael D Stone
Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein...
February 2017: RNA
https://www.readbyqxmd.com/read/28096443/stem-loop-rna-labeling-can-affect-nuclear-and-cytoplasmic-mrna-processing
#12
Stephanie Heinrich, Corinne L Sidler, Claus M Azzalin, Karsten Weis
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level...
February 2017: RNA
https://www.readbyqxmd.com/read/28096424/%C3%AE-actinin-titin-interaction-a-dynamic-and-mechanically-stable-cluster-of-bonds-in-the-muscle-z-disk
#13
Marco Grison, Ulrich Merkel, Julius Kostan, Kristina Djinović-Carugo, Matthias Rief
Stable anchoring of titin within the muscle Z-disk is essential for preserving muscle integrity during passive stretching. One of the main candidates for anchoring titin in the Z-disk is the actin cross-linker α-actinin. The calmodulin-like domain of α-actinin binds to the Z-repeats of titin. However, the mechanical and kinetic properties of this important interaction are still unknown. Here, we use a dual-beam optical tweezers assay to study the mechanics of this interaction at the single-molecule level...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094505/self-assembly-and-disassembly-of-amphiphilic-zwitterionic-perylenediimide-vesicles-for-cell-membrane-imaging
#14
Yong Ye, Yang Zheng, Chendong Ji, Jie Shen, Meizhen Yin
Animal cells have complicated dynamics of cell membrane structures which require desirable dyes to in vivo imaging. Here, an asymmetric amphiphilic zwitterionic perylenediimide (ZP) has been constructed by introducing an octyl chain and a zwitterionic head to each imide position of perylenediimide chromophore. ZP can self-assemble into vesicles in aqueous solution. The aggregated ZP vesicles have been explored to image cell inner or surface membrane structures by controlled disassembly process. The ZP vesicles, when are uptaken into cells, disassemble into single molecules and incorporate into cell inner membranes...
January 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28094382/the-supercoiling-state-of-dna-determines-the-handedness-of-both-h3-and-cenp-a-nucleosomes
#15
R Vlijm, S H Kim, P L De Zwart, Y Dalal, C Dekker
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core...
January 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28092942/advances-in-structural-and-single-molecule-methods-for-investigating-dna-lesion-bypass-and-repair-polymerases
#16
Austin T Raper, Andrew J Reed, Varun V Gadkari, Zucai Suo
Innovative advances in X-ray crystallography and single-molecule biophysics have yielded unprecedented insight into the mechanisms of DNA lesion bypass and damage repair. Time-dependent X-ray crystallography has been successfully applied to view the bypass of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major oxidative DNA lesion, and the incorporation of the triphosphate form, 8-oxo-dGTP, catalyzed by human DNA polymerase β. Significant findings of these studies are highlighted here, and their contributions to the current mechanistic understanding of mutagenic translesion DNA synthesis (TLS) and base excision repair are discussed...
January 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28092434/3d-probed-lipid-dynamics-in-small-unilamellar-vesicles
#17
Meng-Hsuan Chao, Yen-Ting Lin, Namasivayam Dhenadhayalan, Hsin-Lung Lee, Hsin-Yen Lee, King-Chuen Lin
Single-molecule fluorescence correlation spectroscopy overcomes the resolution barrier of optical microscopy (10≈-20 nm) and is utilized to look into lipid dynamics in small unilamellar vesicles (SUVs; diameter < 100 nm). The fluorescence trajectories of lipid-like tracer 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine (DiD) in the membrane bilayers are acquired at a single-molecule level. The autocorrelation analysis yields the kinetic information on lipid organization, oxygen transport, and lateral diffusion in SUVs' membrane...
January 16, 2017: Small
https://www.readbyqxmd.com/read/28092263/transcription-leads-to-pervasive-replisome-instability-in-bacteria
#18
Sarah Mangiameli, Christopher N Merrikh, Paul A Wiggins, Houra Merrikh
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%)...
January 16, 2017: ELife
https://www.readbyqxmd.com/read/28092052/real-time-single-molecule-visualization-of-sh2-domain-membrane-recruitment-in-growth-factor-stimulated-cells
#19
Dongmyung Oh
In the last decade, single molecule tracking (SMT) techniques have emerged as a versatile tool for molecular cell biology research. This approach allows researchers to monitor the real-time behavior of individual molecules in living cells with nanometer and millisecond resolution. As a result, it is possible to visualize biological processes as they occur at a molecular level in real time. Here we describe a method for the real-time visualization of SH2 domain membrane recruitment from the cytoplasm to epidermal growth factor (EGF) induced phosphotyrosine sites on the EGF receptor...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091541/apelin-receptor-homodimer-oligomers-revealed-by-single-molecule-imaging-and-novel-g-protein-dependent-signaling
#20
Xin Cai, Bo Bai, Rumin Zhang, Chunmei Wang, Jing Chen
The apelin receptor (APJ) belongs to family A of the G protein-coupled receptors (GPCRs) and is a potential pharmacotherapeutic target for heart failure, hypertension, and other cardiovascular diseases. There is evidence APJ heterodimerizes with other GPCRs; however, the existence of APJ homodimers and oligomers remains to be investigated. Here, we measured APJ monomer-homodimer-oligomer interconversion by monitoring APJ dynamically on cells and compared their proportions, spatial arrangement, and mobility using total internal reflection fluorescence microscopy, resonance energy transfer, and proximity biotinylation...
January 16, 2017: Scientific Reports
keyword
keyword
67788
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"