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https://www.readbyqxmd.com/read/28204648/ligand-modulated-folding-of-the-full-length-adenine-riboswitch-probed-by-nmr-and-single-molecule-fret-spectroscopy
#1
Sven Warhaut, Klara Rebecca Mertinkus, Philipp Höllthaler, Boris Fürtig, Mike Heilemann, Martin Hengesbach, Harald Schwalbe
No abstract text is available yet for this article.
February 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28199849/quantitative-flim-fret-microscopy-to-monitor-nanoscale-chromatin-compaction-in%C3%A2-vivo-reveals-structural-roles-of-condensin-complexes
#2
David Llères, Aymeric P Bailly, Aurélien Perrin, David G Norman, Dimitris P Xirodimas, Robert Feil
How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells...
February 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28196544/diagnostic-error-in-the-emergency-department-follow-up-of-patients-with-minor-trauma-in-the-outpatient-clinic
#3
Pieter-Jan Moonen, Luc Mercelina, Willem Boer, Tom Fret
BACKGROUND: The Emergency Department (ED) is prone to diagnostic error. Most frequent diagnostic errors involved "minor" trauma. Our goal was to determine how frequently a missed diagnosis was detected during follow up and to determine the frequency and causes of primary missed diagnosis and diagnostic error. METHODS: A retrospective single centre study review, during 6 months including all patients presenting to the outpatient clinic after ED admission with a minor trauma...
February 14, 2017: Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine
https://www.readbyqxmd.com/read/28195691/the-gcamp-r-family-of-genetically-encoded-ratiometric-calcium-indicators
#4
Jung-Hwa Cho, Carter J Swanson, Jeannie Chen, Ang Li, Lisa G Lippert, Shannon E Boye, Kasey Rose, Sivaraj Sivaramakrishnan, Cheng-Ming Chuong, Robert H Chow
We report on GCaMP-Rs, a new family of genetically encoded ratiometric calcium indicators that extend the virtues of the GCaMP proteins to ratiometric measurements. We have engineered a tandem construct of calcium-dependent GCaMP and calcium-independent mCherry fluorescent proteins. The tandem design assures that the two proteins localize in the same cellular compartment(s) and facilitates pixelwise ratiometric measurements; however, Förster resonance energy transfer (FRET) between the fluorophores reduces brightness of the sensor by up to half (depending on the GCaMP variant)...
February 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28194871/engineering-of-optically-encoded-microbeads-with-fret-free-spatially-separated-quantum-dot-layers-for-multiplexed-assays
#5
Igor Nabiev, Regina S Bilan, Viktor A Krivenkov, Mikhail A Berestovoy, Anton Efimov, Igor I Agapov, Pavel S Samokhvalov, Alyona V Sukhanova
Quantum dot (QD)-encoded microbeads are emerging for multiplexed analysis of biological markers. Quantitative encoding of the microbeads prepared with the different concentrations of QDs of different colors suffers from the resonance energy transfer from the QDs fluorescing at the shorter wavelengths to the QDs fluorescing at the longer wavelengths. Here, we have used the layer-by-layer deposition technique to spatially separate QDs of different colors with several polymer layers, so that the distance between them would be larger than the Förster energy transfer radius...
February 13, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28193781/real-time-imaging-of-sodium-glucose-transporter-sglt1-trafficking-and-activity-in-single-cells
#6
Chiara Ghezzi, Guillaume Calmettes, Pauline Morand, Bernard Ribalet, Scott John
The processes controlling targeting of glucose transporters to apical and basolateral membranes of polarized cells are complex and not-well understood. We have engineered SGLT1 and GLUT4 constructs linked to fluorescent proteins to highlight the differences in transporter expression and trafficking, in real time, in different cell types. Activity was assessed in parallel using a FRET glucose sensor. In COS cells and HEK cells, SGLT1 was distributed between the plasma membrane and intracellular compartments, but there was little expression in CHO cells...
February 2017: Physiological Reports
https://www.readbyqxmd.com/read/28193042/using-nanoliposomes-to-construct-a-fret-based-ratiometric-fluorescent-probe-for-sensing-intracellular-ph-values
#7
Yangyang Zhang, Shilei Li, Zhenwen Zhao
Nanoliposomes were first used to encapsulate two fluorophores, fluorescein and cresyl violet, to construct a FRET-based ratiometric fluorescent probe, for sensing intracellular pH values. The morphology, stability, interference factors, biocompatibility, and performance were investigated in detail. The fluorophores-encapsulated nanoliposomes (FEN) probe can be uptaken by cells within 30 min, which is faster than any other nanosensor, and cell viability was not significantly changed upon treatment with the FEN probe for 24 h, showing the low cytotoxicity and good biocompatibility of the probe...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28192309/fret-study-in-oligopeptide-linked-donor-acceptor-system-in-pva-matrix
#8
Sunil Shah, Wlodek Mandecki, Ji Li, Zygmunt Gryczynski, Julian Borejdo, Ignacy Gryczynski, Rafal Fudala
An oligopeptide: Lys-Gly-Pro-Arg-Ser-Leu-Ser-Gly-Lys-NH2, cleaved specifically by a matrix metalloproteinase 9 (MMP-9) at the Ser-Leu bond, was labeled on the ε-NH2 groups of lysine with donor (5, 6 TAMRA) and acceptor (HiLyte647) dye. The donor control was a peptide labeled with 5, 6 TAMRA only on the C-terminal lysine, and the acceptor control was free HiLyte647. Following three products were studied by dissolving in 10% (w/w) poly(vinyl alcohol) and dried on glass slides forming 200 micron films. Absorption spectra of the films show full additivity of donor and acceptor absorptions...
December 13, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28192306/a-molecularly-imprinted-polymer-coated-cdte-quantum-dot-nanocomposite-for-tryptophan-recognition-based-on-the-f%C3%A3-rster-resonance-energy-transfer-process
#9
Antonio Tirado-Guizar, Francisco Paraguay-Delgado, Georgina E Pina-Luis
A new 'turn-on' Förster resonance energy transfer (FRET) nanosensor for l-tryptophan based on molecularly imprinted quantum dots (QDs) is proposed. The approach combines the advantages of the molecular imprinting technique, the fluorescent characteristics of the QDs and the energy transfer process. Silica-coated CdTe QDs were first synthesized and then molecularly imprinted using a sol-gel process without surfactants. The final composite presents stable fluorescence which increases with the addition of l-tryptophan...
November 17, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28192301/dynamic-interaction-between-actin-and-nesprin2-maintain-the-cell-nucleus-in-a-prestressed-state
#10
Abhishek Kumar, G V Shivashankar
Mechanical coupling between the nucleus and the cytoskeleton is indispensable for direct force transduction from the extra cellular matrix (ECM) to the chromatin. Although this physical coupling has been shown to be crucial for nuclear positioning and its function, the quantification of nuclear-cytoskeleton interaction has been lacking. In this paper, using various quantitative fluorescence spectroscopy techniques, we investigate the nature of this connection. High-resolution 3D imaging shows that nesprin2G forms short linear structures along actin stress fibers (ASFs) in the apical region of the nucleus...
November 11, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28192291/understanding-disordered-and-unfolded-proteins-using-single-molecule-fret-and-polymer-theory
#11
Hagen Hofmann
Understanding protein folding and the functional properties of intrinsically disordered proteins (IDPs) requires detailed knowledge of the forces that act in polypeptide chains. These forces determine the dimensions and dynamics of unfolded and disordered proteins and have been suggested to impact processes such as the coupled binding and folding of IDPs, or the rate of protein folding reactions. Much of the progress in understanding the physical and chemical properties of unfolded and intrinsically disordered polypeptide chains has been made possible by the recent developments in single-molecule fluorescence techniques...
November 17, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28191937/a-versatile-platform-for-the-synthesis-of-orthogonally-cleavable-heteromultifunctional-crosslinkers
#12
Michelle R Sorkin, Joshua A Walker, Joseph S Brown, Christopher A Alabi
Cleavable and heteromultifunctional crosslinkers have proven critical in a wide range of biological applications. Traditional approaches for synthesizing these linkers suffer from various synthetic and functional limitations. In this work, an efficient sequence-defined synthetic methodology, developed for the assembly of oligothioetheramides, was used to address many of these limitations. Four heterotrifunctional crosslinkers with up to two orthogonal internal cleavage sites were synthesized. These linkers were conjugated to a pair of fluorophores that undergo Förster resonance energy transfer (FRET) and a model protein - human transferrin...
February 13, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28191892/mechanism-and-timing-of-mcm2-7-ring-closure-during-dna-replication-origin-licensing
#13
Simina Ticau, Larry J Friedman, Kanokwan Champasa, Ivan R Corrêa, Jeff Gelles, Stephen P Bell
The opening and closing of two ring-shaped Mcm2-7 DNA helicases is necessary to license eukaryotic origins of replication, although the mechanisms controlling these events are unclear. The origin-recognition complex (ORC), Cdc6 and Cdt1 facilitate this process by establishing a topological link between each Mcm2-7 hexamer and origin DNA. Using colocalization single-molecule spectroscopy and single-molecule Förster resonance energy transfer (FRET), we monitored ring opening and closing of Saccharomyces cerevisiae Mcm2-7 during origin licensing...
February 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28190830/f%C3%A3-rster-resonance-energy-transfer-mediated-photoluminescence-quenching-in-stoichiometrically-assembled-cdse-zns-quantum-dot-peptide-labeled-black-hole-quencher-conjugates-for-matrix-metalloproteinase-2-sensing
#14
Sreenadh Sasidharan Pillai, Hiroshi Yukawa, Daisuke Onoshima, Vasudevanpillai Biju, Yoshinobu Baba
The steady state and time-resolved photoluminescence quenching of streptavidin modified CdSe/ZnS quantum dots (QDs) instigated by biotin-peptide-BHQ-1 (biotin-pep-BHQ-1) molecule was investigated. Here, we have achieved an efficient photoluminescence (PL) quenching of QDs with the conjugation of dark quencher (black hole quencher-BHQ) molecules intermediated with the GPLGVRGK peptide. The luminescence of streptavidin-QDs585 was decreased upon titration with a nano molar concentration of the biotin-GPLGVRGK-BHQ-1 molecule...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28188294/understanding-the-fret-signatures-of-interacting-membrane-proteins
#15
Christopher King, Valerica Raicu, Kalina Hristova
Forster Resonant Energy Transfer (FRET) is an indispensable experimental tool for studying membrane proteins. Currently, two models are available for researchers to determine the oligomerization state of membrane proteins in a static quenching FRET experiment: the model of Veatch and Stryer derived in 1977, and the Kinetic Theory-based model for intra-oligomeric FRET, derived in 2007. Because of confinement in two-dimensions, a substantial amount of FRET is generated by energy transfer between fluorophores located in separate oligomers in the 2-D bilayer...
February 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28187434/interface-between-breast-cancer-cells-and-the-tumor-microenvironment-using-platelet-rich-plasma-to-promote-tumor-angiogenesis-influence-of-platelets-and-fibrin-bundles-on-the-behavior-of-breast-tumor-cells
#16
Sheila Siqueira Andrade, Joana Tomomi Sumikawa, Eloísa Dognani Castro, Fabricio Pereira Batista, Edgar Paredes-Gamero, Lilian Carolina Oliveira, Izabel Monastério Guerra, Giovani Bravin Peres, Renan Pelluzzi Cavalheiro, Luiz Juliano, Afonso Pinto Nazário, Gil Facina, Siu Mui Tsai, Maria Luiza Vilela Oliva, Manoel João Batista Castello Girão
Cancer progression is associated with an evolving tissue interface of direct epithelial-tumor microenvironment interactions. In biopsies of human breast tumors, extensive alterations in molecular pathways are correlated with cancer staging on both sides of the tumor-stroma interface. These interactions provide a pivotal paracrine signaling to induce malignant phenotype transition, the epithelial-mesenchymal transition (EMT). We explored how the direct contact between platelets-fibrin bundles primes metastasis using platelet-rich plasma (PRP) as a source of growth factors and mimics the provisional fibrin matrix between actively growing breast cancer cells and the tumor stroma...
February 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28186755/thieno-3-2-b-pyrrole-5-carboxamides-as-new-reversible-inhibitors-of-histone-lysine-demethylase-kdm1a-lsd1-part-1-high-throughput-screening-and-preliminary-exploration
#17
Luca Sartori, Ciro Mercurio, Federica Amigoni, Anna Cappa, Giovanni Fagá, Raimondo Fattori, Elena Legnaghi, Giuseppe Ciossani, Andrea Mattevi, Giuseppe Meroni, Loris Moretti, Valentina Cecatiello, Sebastiano Pasqualato, Alessia Romussi, Florian Thaler, Paolo Trifiró, Manuela Villa, Stefania Vultaggio, Oronza A Botrugno, Paola Dessanti, Saverio Minucci, Elisa Zagarrí, Daniele Carettoni, Lucia Iuzzolino, Mario Varasi, Paola Vianello
Lysine specific demethylase 1 KDM1A (LSD1) is one regulator of histone methylation and it is increasingly recognized as a potential therapeutic target in oncology. We report on a high-throughput screening campaign performed on KDM1A/CoREST, using a time resolved fluorescence resonance energy transfer (TR-FRET) technology, to identify reversible inhibitors. The screening led to 115 hits for which we determined biochemical IC50, thus identifying 4 chemical series. After data analysis, we have prioritized the chemical series of N-phenyl-4H-thieno[3, 2-b]pyrrole-5-carboxamide for which we obtained X-ray structures of the most potent hit (compound 19, IC50 = 2...
February 10, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28186491/combinatorial-bzip-dimers-define-complex-dna-binding-specificity-landscapes
#18
Jose A Rodriguez-Martinez, Aaron W Reinke, Devesh Bhimsaria, Amy E Keating, Aseem Z Ansari
How transcription factor dimerization impacts DNA binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers...
February 10, 2017: ELife
https://www.readbyqxmd.com/read/28182975/fluorescent-on-off-on-switching-sensor-based-on-cdte-quantum-dots-coupled-with-multiwalled-carbon-nanotubes-graphene-oxide-nanoribbons-for-simultaneous-monitoring-of-dual-foreign-dnas-in-transgenic-soybean
#19
Yaqi Li, Li Sun, Jing Qian, Lingliang Long, Henan Li, Qian Liu, Jianrong Cai, Kun Wang
With the increasing concern of potential health and environmental risk, it is essential to develop reliable methods for transgenic soybean detection. Herein, a simple, sensitive and selective assay was constructed based on homogeneous fluorescence resonance energy transfer (FRET) between CdTe quantum dots (QDs) and multiwalled carbon nanotubes@graphene oxide nanoribbons (MWCNTs@GONRs) to form the fluorescent "on-off-on" switching for simultaneous monitoring dual target DNAs of promoter cauliflower mosaic virus 35s (P35s) and terminator nopaline synthase (TNOS) from transgenic soybean...
January 28, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28181555/determination-of-biological-activity-of-gonadotropins-hcg-and-fsh-by-f%C3%A3-rster-resonance-energy-transfer-based-biosensors
#20
Olga Mazina, Anni Allikalt, Juha S Tapanainen, Andres Salumets, Ago Rinken
Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Förster resonance energy transfer (FRET) biosensor protein (T)Epac(VV) in living cells upon activation of the relevant gonadotropin receptor...
February 9, 2017: Scientific Reports
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