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https://www.readbyqxmd.com/read/29334220/computational-design-synthesis-and-structure-property-evaluation-of-1-3-thiazole-based-colour-tunable-multiheterocyclic-small-organic-fluorophores-as-multifunctional-molecular-materials
#1
Rakesh Radhakrishnan, Kumaran G Sreejalekshmi
Probing chemical space of luminescent organic materials built on novel cores is highly imperative for its potential to expand the horizons of advanced functional materials. Small organic fluorophores possessing therapeutic traits can contribute to theranostics. We coupled computational and classical synthetic chemistry strategies for the rational design of 5-(hetero-2-yl)-1,3-thiazoles as colour tunable fluorophore core. With the aid of DFT and TD-DFT, we prove multiheterocyclic system built on thiazole-het core with three inherent tunable sites on thiazole (C2, C4 and C5) capable of accommodating panoply of substituents, as a multifunctional molecular materials' platform...
January 15, 2018: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29334187/surveying-the-landscape-of-optogenetic-methods-for-detection-of-protein-protein-interactions
#2
REVIEW
Matthew D Wiens, Robert E Campbell
Mapping the protein-protein interaction (PPi) landscape is of critical importance to furthering our understanding how cells and organisms function. Optogenetic methods, that is, approaches that utilize genetically encoded fluorophores or fluorogenic enzyme reactions, uniquely enable the visualization of biochemical phenomena in live cells with high spatial and temporal accuracy. Applying optogenetic methods to the detection of PPis requires the engineering of protein-based systems in which an optical signal undergoes a substantial change when the two proteins of interest interact...
January 15, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29334105/specific-labeling-of-mitochondria-of-chlamydomonas-with-cationic-helicene-fluorophores
#3
Christoph Bauer, Romain Duwald, Geraldine Maria Labrador, Simon Pascal, Pau Moneva Lorente, Johann Bosson, Jérôme Lacour, Jean-David Rochaix
Twelve cationic helicenes and one triangulene were tested for the specific labeling of mitochondria from algal cells. Octyl ester derivative 5 readily penetrates algal cells and gives rise to clear fluorescence patterns when it is used at concentrations in the μM range. Under these conditions, cell structures are well preserved and cell survival is not compromised. Cationic helicene compounds such as 5 provide new useful tools for examining the mitochondrial network and its dynamics including fission and fusion events...
January 15, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29332829/synchronous-detection-of-ebolavirus-conserved-rna-sequences-and-ebolavirus-encoded-mirna-like-fragment-based-on-a-zwitterionic-copper-ii-metal-organic-framework
#4
Gui-Hua Qiu, Zi-Hua Weng, Pei-Pei Hu, Wen-Jun Duan, Bao-Ping Xie, Bin Sun, Xiao-Yan Tang, Jin-Xiang Chen
From a three-dimensional (3D) metal-organic framework (MOF) of {[Cu(Cmdcp)(phen)(H2O)]2·9H2O}n (1, H3CmdcpBr = N-carboxymethyl-(3,5-dicarboxyl)pyridinium bromide, phen = phenanthroline), a sensitive and selective fluorescence sensor has been developed for the simultaneous detection of ebolavirus conserved RNA sequences and ebolavirus-encoded microRNA-like (miRNA-like) fragment. The results from molecular dynamics simulation confirmed that MOF 1 absorbs carboxyfluorescein (FAM)-tagged and 5(6)-carboxyrhodamine, triethylammonium salt (ROX)-tagged probe ss-DNA (probe DNA, P-DNA) by π…π stacking and hydrogen bonding, as well as additional electrostatic interactions to form a sensing platform of P-DNAs@1 with quenched FAM and ROX fluorescence...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29332818/a-novel-dual-labeling-approach-enables-converting-fluorescence-labeling-reagents-into-fluorogenic-ones-via-introduction-of-purification-tags-application-to-determination-of-glyoxylic-acid-in-serum
#5
Mahmoud El-Maghrabey, Masaki Mine, Naoya Kishikawa, Kaname Ohyama, Naotaka Kuroda
Pre-column derivatization with fluorescence labeling reagents involves many problems including crowded chromatograms, possibility of the introduction of analytical errors, and poor selectivity. Herein we report a novel purification tag/fluorophore dual labeling approach based on a multi-component reaction to solve this major problem. Glyoxylic acid was recently identified as an early biomarker for diabetes, thus it was selected as a model analyte for our new dual labeling approach. Using the multi-component Petasis reaction, we could introduce a fluorophore (1-pyreneboronic acid, 1-PyBA) and a purification tag (taurine) to our target analyte (glyoxylic acid) in one step reaction...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29330789/fluorescence-lifetime-imaging-microscopy-flim-as-a-tool-to-investigate-hypoxia-induced-protein-protein-interaction-in-living-cells
#6
Vera Schützhold, Joachim Fandrey, Katrin Prost-Fingerle
Fluorescence resonance energy transfer (FRET) is widely used as a method to investigate protein-protein interactions in living cells. A FRET pair donor fluorophore in close proximity to an appropriate acceptor fluorophore transfers emission energy to the acceptor, resulting in a shorter lifetime of the donor fluorescence. When the respective FRET donor and acceptor are fused with two proteins of interest, a reduction in donor lifetime, as detected by fluorescence lifetime imaging microscopy (FLIM), can be taken as proof of close proximity between the fluorophores and therefore interaction between the proteins of interest...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29330463/effective-photo-enhancement-of-cellular-activity-of-fluorophore-octaarginine-antisense-pna-conjugates-correlates-with-singlet-oxygen-formation-endosomal-escape-and-chromophore-lipophilicity
#7
Reza Yarani, Takehiko Shiraishi, Peter E Nielsen
Photochemical internalization (PCI) is a cellular drug delivery method based on the generation of light-induced reactive oxygen species (ROS) causing damage to the endosomal membrane and thereby resulting in drug release to the cytoplasm. In our study a series of antisense fluorophore octaarginine peptide nucleic acid (PNA) conjugates were investigated in terms of PCI assisted cellular activity. It is found that tetramethylrhodamine and Alexa Fluor 555 conjugated octaarginine PNA upon irradiation exhibit more than ten-fold increase in antisense activity in the HeLa pLuc705 luciferase splice correction assay...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330182/fluorescence-recovery-allows-the-implementation-of-a-fluorescence-reporter-gene-platform-applicable-for-the-detection-and-quantification-of-horizontal-gene-transfer-in-anoxic-environments
#8
Rafael Pinilla, Leise Riber, Søren J Sørensen
The study of horizontal gene transfer (HGT) in microbial communities has been revolutionized by significant advances in cultivation-independent methods based on fluorescence reporter gene technologies. Recently, the combination of these novel approaches with flow cytometry has presented itself as one of the most powerful tools to study the spread of mobile genetic elements (MGEs) in the environment. However, the use of fluorescent markers like green fluorescent protein (GFP) and mCherry is limited by environmental constraints that affect the correct maturation of their fluorophores, such as oxygen availability and pH levels...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29328675/design-synthesis-and-evaluation-of-n-and-c-terminal-protein-bioconjugates-as-gpcr-agonists
#9
Robert D Healey, Jonathan Wojciechowski, Ana Monserrat-Martinez, Susan L Tan, Christopher P Marquis, Emma Sierecki, Yann Gambin, Angela Monique Finch, Pall Thordarson
A GPCR agonist protein, thaumatin, was site-specifically conjugated at the N- or C-terminus with a fluorophore for visualization of GPCR:agonist interactions. The N-terminus was specifically conjugated using a synthetic 2 pyridinecarboxyaldehyde reagent. The interaction profiles observed for N- and C-terminal conjugates were varied; N-terminal conjugates interacted very weakly with the GPCR of interest, whereas C-terminal conjugates bound to the receptor. These chemical biology tools allow interactions of therapeutic proteins:GPCR to be monitored and visualized...
January 12, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29328673/fluorescent-proteins-detect-host-structural-rearrangements-via-electrostatic-mechanism
#10
Lena Simine, Heiko Lammert, Li Sun, Jose Nelson Onuchic, Peter J Rossky
The rational design of genetically encoded fluorescent bio-sensors, which can detect rearrangements of target proteins via interdomain allostery, is hindered by the absence of mechanistic understanding of the underlying photo-physics. Here, we focus on the modulation of fluorescence by mechanical perturbation in a popular biological probe: enhanced Green Fluorescent Protein (eGFP). Using a combination of molecular dynamics (MD) simulations and quantum chemistry, and a set of physically motivated assumptions, we construct a map of fluorescence quantum yield as a function of a 2D electric field imposed by the protein environment on the fluorophore...
January 12, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29328626/polystyrene-core-silica-shell-scintillant-nanoparticles-for-low-energy-radionuclide-quantification-in-aqueous-media
#11
Colleen M Janczak, Isen A C Calderon, Zeinab Mokhtari, Craig Alan Aspinwall
β-particle emitting radionuclides are useful molecular labels due to their abundance in biomolecules. Detection of -emission from 3H, 35S, and 33P, important biological isotopes, is challenging due to the low energies (Emax ≤ 300 keV) and short penetration depths (≤ 0.6 mm) in aqueous media. The activity of biologically relevant β-emitters is usually measured in liquid scintillation cocktail (LSC), a mixture of energy-absorbing organic solvents, surfactants, and scintillant fluorophores, which places significant limitations on the ability to acquire time-resolved measurements directly in aqueous biological systems...
January 12, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29326071/a-rapid-fluorescent-method-for-the-real-time-measurement-of-poly-adp-ribose-polymerase-1-activity
#12
T A Kurgina, R O Anarbaev, M V Sukhanova, O I Lavrik
Poly(ADP-ribose) polymerase 1 (PARP1) is a key enzyme that regulates important cellular processes, including DNA repair. PARP1 binds to a DNA damage site and synthesizes poly(ADP-ribose) chains (PARs), which serve as a signal of DNA damage for other DNA repair enzymes. PARP1 is a recognized target for the development of anti-cancer drugs. In this work, a method is developed that makes it possible to investigate the complex formation of PARP1 with DNA as well as its dissociation by detecting the fluorescence anisotropy of this complex during the poly(ADP-ribose) synthesis...
January 8, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29324833/evidence-for-pmat-and-oct-like-biogenic-amine-transporters-in-a-probiotic-strain-of-lactobacillus-implications-for-interkingdom-communication-within-the-microbiota-gut-brain-axis
#13
Mark Lyte, David R Brown
The ability of prokaryotic microbes to produce and respond to neurochemicals that are more often associated with eukaryotic systems is increasingly recognized through the concept of microbial endocrinology. Most studies have described the phenomena of neurochemical production by bacteria, but there remains an incomplete understanding of the mechanisms by which microbe- or host-derived neuroactive substances can be recognized by bacteria. Based on the evolutionary origins of eukaryotic solute carrier transporters, we hypothesized that bacteria may possess an analogous uptake function for neuroactive biogenic amines...
2018: PloS One
https://www.readbyqxmd.com/read/29323474/caspase-1-specific-light-up-probe-with-aggregation-induced-emission-characteristics-for-inhibitor-screening-of-coumarin-originated-natural-products
#14
Hao Lin, Haitao Yang, Shuai Huang, Fujia Wang, Dong-Mei Wang, Bin Liu, Yi-Da Tang, Chong-Jing Zhang
Caspase-1 is a key player in pyroptosis and inflammation. Caspase-1 inhibition is found to be beneficial to various diseases. Coumarin-originated natural products have an anti-inflammation function, but their direct inhibition effect to caspase-1 remains unexplored. To evaluate their interactions, the widely used commercial coumarin-based probe (Ac-YVAD-AMC) is not suitable, as the background signal from coumarin-originated natural products could interfere with the screening results. Therefore, fluorescent probes using a large Stokes shift could help solve this problem...
January 11, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29322581/technical-implementations-of-light-sheet-microscopy
#15
REVIEW
Zagato Elisa, Brans Toon, Stefaan C De Smedt, Remaut Katrien, Neyts Kristiaan, Braeckmans Kevin
Fluorescence-based microscopy is among the most successful methods in biological studies. It played a critical role in the visualization of subcellular structures and in the analysis of complex cellular processes, and it is nowadays commonly employed in genetic and drug screenings. Among the fluorescence-based microscopy techniques, light sheet fluorescence microscopy (LSFM) has shown a quite interesting set of benefits. The technique combines the speed of epi-fluorescence acquisition with the optical sectioning capability typical of confocal microscopes...
January 11, 2018: Microscopy Research and Technique
https://www.readbyqxmd.com/read/29322426/isolation-and-characterization-of-mouse-intrahepatic-lymphocytes-by-flow-cytometry
#16
Florian Wiede, Tony Tiganis
In the field of cellular immunology multicolor flow cytometry is a frequently applied method that allows for the simultaneously detection of multiple parameters on an individual cell basis. Flow cytometry can be used to characterize a wide range of immune cell subsets using fluorophore-conjugated antibodies to a wide range of cellular antigens. The isolation of immune cells from nonlymphoid tissue and their preparation for flow cytometry can be a challenging process with respect to immune cell yields and viability...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29320928/interaction-of-caffeine-and-sulfadiazine-with-lysozyme-adsorbed-at-colloidal-metal-nanoparticle-interface-influence-on-drug-transport-ability-and-antibacterial-activity
#17
Vikash K Sonu, Imocha Rajkumar, Kaushik Bhattacharjee, S R Joshi, Sivaprasad Mitra
The modulated bioactivity of proteins immobilized on nanoparticle (NP) interfaces is of tremendous interest towards designing better therapeutic and diagnostic tools. In this work, binding behavior and the antibacterial activity of free lysozyme (LYS) as well as its non-covalent assembly with silver (Ag) and gold (Au) colloidal NPs were compared in presence of two model drugs, viz. sulfadiazine (SDZ) and caffeine (CAF). Intrinsic protein fluorescence was found to quench due to the formation drug-protein complex in case of CAF resulting a linear Stern-Volmer (SV) plot with KSV = 1...
January 11, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29320869/challenges-and-opportunities-for-small-molecule-fluorescent-probes-in-redox-biology-applications
#18
Xiqian Jiang, Lingfei Wang, Shaina Laufer Carroll, Jianwei Chen, Meng C Wang, Jin Wang
SIGNIFICANCE: The concentrations of reactive oxygen/nitrogen species (ROS/RNS) are critical to various biochemical processes. Small molecule fluorescent probes have been widely used to detect and/or quantify ROS/RNS in many redox biology studies and serve as an important complementary to protein-based sensors with unique applications. Recent Advances: New sensing reactions have emerged in probe development allowing more selective and quantitative detection of ROS/RNS, especially in live cells...
January 10, 2018: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29320696/using-a-fret-library-with-multiple-probe-pairs-to%C3%A2-drive-monte-carlo-simulations-of-%C3%AE-synuclein
#19
John J Ferrie, Conor M Haney, Jimin Yoon, Buyan Pan, Yi-Chih Lin, Zahra Fakhraai, Elizabeth Rhoades, Abhinav Nath, E James Petersson
We describe a strategy for experimentally-constraining computational simulations of intrinsically disordered proteins (IDPs), using α-synuclein, an IDP with a central role in Parkinson's disease pathology, as an example. Previously, data from single-molecule Förster Resonance Energy Transfer (FRET) experiments have been effectively utilized to generate experimentally constrained computational models of IDPs. However, the fluorophores required for single-molecule FRET experiments are not amenable to the study of short-range (<30 Å) interactions...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29320445/chlorophyll-inspired-red-region-fluorophores-building-block-synthesis-and-studies-in-aqueous-media
#20
Rui Liu, Mengran Liu, Don Hood, Chih-Yuan Chen, Christopher J MacNevin, Dewey Holten, Jonathan S Lindsey
Fluorophores that absorb and emit in the red spectral region (600-700 nm) are of great interest in photochemistry and photomedicine. Eight new target chlorins (and 19 new chlorins altogether)-analogues of chlorophyll-of different polarities have been designed and synthesized for various applications; seven of the chlorins are equipped with a bioconjugatable tether. Hydrophobic or amphiphilic chlorins in a non-polar organic solvent (toluene), polar organic solvent (DMF), and aqueous or aqueous micellar media show a sharp emission band in the red region and modest fluorescence quantum yield (Φf = 0...
January 10, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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