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Forster resonance energy transfer

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https://www.readbyqxmd.com/read/28542243/covalent-dye-attachment-influences-the-dynamics-and-conformational-properties-of-flexible-peptides
#1
Manuel P Luitz, Anders Barth, Alvaro H Crevenna, Rainer Bomblies, Don C Lamb, Martin Zacharias
Fluorescence spectroscopy techniques like Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) have become important tools for the in vitro and in vivo investigation of conformational dynamics in biomolecules. These methods rely on the distance-dependent quenching of the fluorescence signal of a donor fluorophore either by a fluorescent acceptor fluorophore (FRET) or a non-fluorescent quencher, as used in FCS with photoinduced electron transfer (PET). The attachment of fluorophores to the molecule of interest can potentially alter the molecular properties and may affect the relevant conformational states and dynamics especially of flexible biomolecules like intrinsically disordered proteins (IDP)...
2017: PloS One
https://www.readbyqxmd.com/read/28542211/f%C3%A3-rster-resonance-energy-transfer-role-of-diffusion-of-fluorophore-orientation-and-separation-in-observed-shifts-of-fret-efficiency
#2
Bram Wallace, Paul J Atzberger
Förster resonance energy transfer (FRET) is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. However, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged...
2017: PloS One
https://www.readbyqxmd.com/read/28538149/icon-an-adaptation-of-infinite-hmms-for-time-traces-with-drift
#3
Ioannis Sgouralis, Steve Pressé
Bayesian nonparametric methods have recently transformed emerging areas within data science. One such promising method, the infinite hidden Markov model (iHMM), generalizes the HMM that itself has become a workhorse in single molecule data analysis. The iHMM goes beyond the HMM by self-consistently learning all parameters learned by the HMM in addition to learning the number of states without recourse to any model selection steps. Despite its generality, simple features (such as drift), common to single molecule time traces, result in an overinterpretation of drift and the introduction of artifact states...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28528543/plasmon-enhanced-energy-transfer-in-photosensitive-nanocrystal-device
#4
Shahab Akhavan, Mehmet Zafer Akgul, Pedro Ludwig Hernandez Martinez, Hilmi Volkan Demir
Förster resonance energy transfer (FRET) interacted with localized surface plasmon (LSP) gives us the ability to overcome inadequate transfer of energy between donor and acceptor nanocrystals (NCs). In this paper, we show LSP-enhanced FRET in colloidal photosensors of NCs in operation, resulting in substantially enhanced photosensitivity. The proposed photosensitive device is a layered self-assembled colloidal platform consisting of separated monolayers of the donor and the acceptor colloidal NCs with an intermediate metal nanoparticle (MNP) layer made of gold inter-spaced by polyelectrolyte layers...
May 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28528252/investigation-of-the-binding-affinity-in-vitamin-b12-bovine-serum-albumin-system-using-various-spectroscopic-methods
#5
Magdalena Makarska-Bialokoz
The binding affinity between vitamin B12 (VitB12) and bovine serum albumin (BSA) has been investigated in aqueous solution at pH=7.4, employing UV-vis absorption and steady-state, synchronous and three-dimensional fluorescence spectra techniques. Representative effects noted for BSA intrinsic fluorescence resulting from the interactions with VitB12 confirm the formation of π-π stacked non-covalent and non-fluorescent complexes in the system VitB12-BSA. All the determined parameters, the binding, fluorescence quenching and bimolecular quenching rate constants (of the order of 10(4)Lmol(-1), 10(3)Lmol(-1) and 10(11)Lmol(-1)s(-1), respectively), as well as Förster resonance energy transfer parameters validate the mechanism of static quenching...
May 11, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28524818/fluorescence-lifetime-imaging-microscopy-reveals-rerouting-of-snare-trafficking-driving-dendritic-cell-activation
#6
Daniëlle Rianne José Verboogen, Natalia González Mancha, Martin Ter Beest, Geert van den Bogaart
SNARE proteins play a crucial role in intracellular trafficking by catalyzing membrane fusion, but assigning SNAREs to specific intracellular transport routes is challenging with current techniques. We developed a novel Förster resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM)-based technique allowing visualization of real-time local interactions of fluorescently tagged SNARE proteins in live cells. We used FRET-FLIM to delineate the trafficking steps underlying the release of the inflammatory cytokine interleukin-6 (IL-6) from human blood-derived dendritic cells...
May 19, 2017: ELife
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#7
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28510311/rapid-microfluidic-dilution-for-single-molecule-spectroscopy-of-low-affinity-biomolecular-complexes
#8
Niels Zijlstra, Fabian Dingfelder, Bengt Wunderlich, Franziska Zosel, Stephan Benke, Daniel Nettels, Benjamin Schuler
To enable the investigation of low-affinity biomolecular complexes with confocal single-molecule spectroscopy, we have developed a microfluidic device that allows a concentrated sample to be diluted by up to five orders of magnitude within milliseconds, at the physical limit dictated by diffusion. We demonstrate the capabilities of the device by studying the dissociation kinetics and structural properties of low-affinity protein complexes using single-molecule two-color and three-color Förster resonance energy transfer (FRET)...
May 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28507674/highly-specific-c-c-bond-cleavage-induced-fret-fluorescence-for-in-vivo-biological-nitric-oxide-imaging
#9
Hua Li, Deliang Zhang, Mengna Gao, Lumei Huang, Longguang Tang, Zijing Li, Xiaoyuan Chen, Xianzhong Zhang
A novel Förster resonance energy transfer (FRET) fluorescence "off-on" system based on the highly specific, sensitive and effective C-C bond cleavage of certain dihydropyridine derivatives was reported for real-time quantitative imaging of nitric oxide (NO). 1,4-Dihydropyridine was synthesized as a novel linker which could connect customized fluorophores and their corresponding quenchers. The specific and quantitative response to NO is confirmed using fluorescence spectrometry with the classical example of fluorescein isothiocyanate (FITC) and [4'-(N,N'-dimethylamino)phenylazo] benzoyl (DABCYL)...
March 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28499172/fluorescence-quenching-study-on-the-interaction-of-ferroferric-oxide-nanoparticles-with-bovine-serum-albumin
#10
Changchun Hao, Guangkuan Xu, Ying Feng, Linhao Lu, Wenyuan Sun, Runguang Sun
Fluorescence quenching was used to study the potential interaction mechanism of Bovine serum albumin (BSA) with either hydrophilic ferroferric oxide (Fe3O4) nanoparticles (NPs) or hydrophobic Fe3O4 NPs. The experimental results indicated the mechanism between BSA and hydrophilic Fe3O4 NPs was static quenching and the one between BSA and hydrophobic Fe3O4 NPs was dynamic process that was drove by Förster's resonance energy transfer (FRET). And the binding parameters for the interaction of BSA with either hydrophilic or hydrophobic Fe3O4 NPs were calculated by using the fluorescence quenching measurement...
May 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28496139/operational-lifetimes-of-organic-light-emitting-diodes-dominated-by-f%C3%A3-rster-resonance-energy-transfer
#11
Hirohiko Fukagawa, Takahisa Shimizu, Yukiko Iwasaki, Toshihiro Yamamoto
Organic light-emitting diodes are a key technology for next-generation information displays because of their low power consumption and potentially long operational lifetimes. Although devices with internal quantum efficiencies of approximately 100% have been achieved using phosphorescent or thermally activated delayed fluorescent emitters, a systematic understanding of materials suitable for operationally stable devices is lacking. Here we demonstrate that the operational stability of phosphorescent devices is nearly proportional to the Förster resonance energy transfer rate from the host to the emitter when thermally activated delayed fluorescence molecules are used as the hosts...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28494963/design-and-properties-of-genetically-encoded-probes-for-sensing-macromolecular-crowding
#12
Boqun Liu, Christoffer Åberg, Floris J van Eerden, Siewert J Marrink, Bert Poolman, Arnold J Boersma
Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Förster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28494950/simultaneous-determination-of-two-subdomain-folding-rates-using-the-transfer-quench-method
#13
Gil Rahamim, Dan Amir, Elisha Haas
The investigation of the mechanism of protein folding is complicated by the context dependence of the rates of intramolecular contact formation. Methods based on site-specific labeling and ultrafast spectroscopic detection of fluorescence signals were developed for monitoring the rates of individual subdomain folding transitions in situ, in the context of the whole molecule. However, each site-specific labeling modification might affect rates of folding of near-neighbor structural elements, and thus limit the ability to resolve fine differences in rates of folding of these elements...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28485436/silver-nanoparticle-plasmonic-enhanced-f%C3%A3-rster-resonance-energy-transfer-fret-imaging-of-protein-specific-sialylation-on-the-cell-surface
#14
Tingbi Zhao, Ting Li, Yang Liu
A large amount of proteins are post-translationally modified with a sialic acid terminal oligosaccharide, and sialylation directly affects the function of glycoproteins and adjusts relevant biological processes. Herein, we developed a method for imaging analysis of protein-specific sialylation on the cell surface via silver nanoparticle (AgNPs) plasmonic enhanced Förster resonance energy transfer (FRET). In this strategy, the target monosaccharide was labelled with the FRET acceptor of Cy5 via bioorthogonal chemistry...
May 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/28483922/quantitative-micro-spectroscopic-imaging-reveals-viral-and-cellular-rna-helicase-interactions-in-live-cells
#15
M J Corby, Michael R Stoneman, Gabriel Biener, Joel D Paprocki, Rajesh Kolli, Valerica Raicu, David N Frick
Human cells detect RNA viruses through a set of helicases called RIG-I like receptors (RLRs) that initiate the interferon response via a mitochondrial signaling complex. Many RNA viruses also encode helicases, which sometimes are covalently linked to proteases that cleave signaling proteins. One unresolved question is how RLRs interact with each other and with viral proteins in cells. This study examined the interactions among the hepatitis C virus (HCV) helicase and RLR helicases in live cells with quantitative micro-spectroscopic imaging (Q-MSI), a technique that determines Forster Resonance Energy Transfer (FRET) efficiency and sub-cellular donor and acceptor concentrations...
May 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28470684/how-to-switch-the-motor-on-rna-polymerase-initiation-steps-at-the-single-molecule-level
#16
REVIEW
M Marchetti, A Malinowska, I Heller, Gijs J L Wuite
RNA polymerase (RNAP) is the central motor of gene expression since it governs the process of transcription. In prokaryotes, this holoenzyme is formed by the RNAP core and a sigma factor. After approaching and binding the specific promoter site on the DNA, the holoenzyme-promoter complex undergoes several conformational transitions that allow unwinding and opening of the DNA duplex. Once the first DNA basepairs (∼10bp) are transcribed in an initial transcription process, the enzyme unbinds from the promoter and proceeds downstream along the DNA while continuously opening the helix and polymerizing the ribonucleotides in correspondence with the template DNA sequence...
May 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28467705/plasmon-coupled-resonance-energy-transfer
#17
Liang-Yan Hsu, Wendu Ding, George C Schatz
In this study, we overview resonance energy transfer between molecules in the presence of plasmonic structures and derive an explicit Förster-type expression for the rate of plasmon-coupled resonance energy transfer (PC-RET). The proposed theory is general for energy transfer in the presence of materials with any space-dependent, frequency-dependent, or complex dielectric functions. Furthermore, the theory allows us to develop the concept of a generalized spectral overlap (GSO) J̃ (the integral of the molecular absorption coefficient, normalized emission spectrum, and the plasmon coupling factor) for understanding the wavelength dependence of PC-RET and to estimate the rate of PC-RET WET...
May 11, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28467088/bridging-lanthanide-to-quantum-dot-energy-transfer-with-a-short-lifetime-organic-dye
#18
Sebastián A Díaz, Guillermo Lasarte Aragonés, Susan Buckhout-White, Xue Qiu, Eunkeu Oh, Kimihiro Susumu, Joseph S Melinger, Alan L Huston, Niko Hildebrandt, Igor L Medintz
Semiconductor nanocrystals or quantum dots (QDs) should act as excellent Förster resonance energy transfer (FRET) acceptors due to their large absorption cross section, tunable emission, and high quantum yields. Engaging this type of FRET can be complicated due to direct excitation of the QD acceptor along with its longer excited-state lifetime. Many cases of QDs acting as energy transfer acceptors are within time-gated FRET from long-lifetime lanthanides, which allow the QDs to decay before observing FRET...
May 3, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28463765/bright-carbon-dots-as-fluorescence-sensing-agents-for-bacteria-and-curcumin
#19
Mirza Muhammad Fahad Baig, Yu-Chie Chen
Carbon dots (C-dots) are fluorescent nanomaterials that possess good photostability and low toxicity. They have been used as sensing probes and bioimaging agents for a variety of biological species. Numerous methods are available to generate C-dots. Nevertheless, simple and straightforward synthesis methods must be explored for the synthesis of C-dots from inexpensive, natural sources. In this study, we developed a simple method to generate C-dots from inexpensive chicken egg whites through a one-step heating reaction...
April 17, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28462837/design-synthesis-and-evaluation-of-1-3-6-trisubstituted-4-oxo-1-4-dihydroquinoline-2-carboxylic-acid-derivatives-as-eta-receptor-selective-antagonists-using-fret-assay
#20
Nikhil Khadtare, Ralph Stephani, Vijaya Korlipara
The endothelin axis and in particular the two receptor subtypes, ETA and ETB, are under investigation for the treatment of various diseases such as pulmonary arterial hypertension, fibrosis, renal failure and cancer. Previous work in our lab has shown that 1,3,6-trisubstituted-4-oxo-1,4-dihydroquinoline-2-carboxylic acid derivatives exhibit noteworthy endothelin receptor antagonist activity. A series of analogues with modifications centered around position 6 of the heterocyclic quinolone core and replacement of the aryl carboxylic acid group with an isosteric tetrazole ring was designed and synthesized to further optimize the structure activity relationship...
April 19, 2017: Bioorganic & Medicinal Chemistry Letters
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