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Dataset results
13 results for “fluorophores”
Examination of protein-like fluorophores in chromophoric dissolved organic matter (CDOM) in a wetland and coastal environment for the wet and dry seasons of the years 2002 and 2003 (FCE)
Water samples are collected at the end of the dry and the wet season from all LTER sites and stored on ice until return to the lab. They are pre-filtered through pre-combusted GF/F filters and ultrafiltered and concentrated with a Pellicon 2 Mini tangential flow ultrafiltration system.Concentrated samples were then analyzed using fluorescence and SEC-HPLC. This CDOM optical study revealed the presence of two classes of compounds associated with the protein-like peak (peak T; excitation/emission (Ex/Em) maxima at around 280 nm/325 nm), which have very different chemical structures and ecological roles. In addition to proteins, we propose phenolic compounds as possible origins of peak T in coastal and wetland environments. In this study, natural water samples were obtained from subtropical rivers and estuarine environments within the Florida Coastal Everglades (FCE) ecosystem. The samples were ultra-filtered and excitation-emission fluorescence matrices (EEMs) were obtained. The EEMs showed the presence of four peaks with Ex/Em maxima at around 280 nm/325 nm (T), less than 260 nm/460 nm (A), 300 nm/412nm (M), and 350 nm/470 nm (C). To better understand the nature of peak T, the components originating this peak were separated using size exclusion chromatography (SEC) and detected by fluorescence emission at Ex/Em = 280 nm/325 nm. The elution curves revealed the presence of two elution peaks at a molecular weight of greater than 50K (void volume; T1) and around 7.6K (T2). This result suggested the need of cautious interpretation in the use of peak T as a proxy for the detection of proteinaceous materials in wetland and estuarine environments, since significant amounts of potentially interfering phenolic compounds are leached from senescent biomass in wetland and coastal ecosystems. As such EEM spectra of gallic acid an important component of hydrolysable tannins, and condensed tannins extracted from red mangroves (Rhizophora mangle) showed the presence of a peak maxima
Photochromic fluorophores enable imaging of endogenous fusion constructs in Candida albicans
<p>10. Gcn5_Stat : Main dataset for figure 2 stationary phase of the manuscript.</p> <p>5., 6. and 7.Gcn5_Stat are additional datasets for figure 2 stationary phase.</p> <p>11. SC5314_Stat : main negative control dataset for figure 2 depicted in supplementary figure 1.</p> <p>14. Gcn5_Exp : Main dataset for figure 2 exponential phase of the manuscript.</p> <p>12., 13. Gcn5_Exp are additional datasets for figure 2 exponential phase.</p> <p>15. SC5314_Exp : main negative control dataset for figure 2 depicted in supplementary figure 1.</p> <p>___________________________________________________________________________________________________</p> <p>2. Erg11 and 7. Erg11 are main datasets for figure 3 of the manuscript.</p> <p>15. SC5314 (Erg11 control) : negative control dataset for figure 3 depicted in supplementary figure 3.</p>
Research data supporting "Probing amylin fibrillation at an early stage via a tetracysteine-recognising fluorophore"
<p>Research data supporting the publication:</p> <p>Wang S. et al., 2017, Talanta, DOI: 10.1016/j.talanta.2017.05.015</p>
Long-Term, Single-Molecule Imaging of Proteins in Live Cells with Photoregulated Fluxional Fluorophores
<p>Supporting data for paper "Long-Term, Single-Molecule Imaging of Proteins in Live Cells with Photoregulated Fluxional Fluorophores"</p>
Mixture of three fluorophores
<p>This data was used in the following publication:</p><p>Anne Bech Risum, Jesper Løve Hinrich and Åsmund Rinnan (2024): Multi-way decomposition followed by reconvolution of fluorescence time decay data, Analytical Chemistry. DOI: 10.1021/acs.analchem.3c00634</p><p>The data is in Matlab format, and a description of the content can be found in the ReadMe.txt file</p>
Source data for: Electrochemically controlled blinking of fluorophores for quantitative STORM imaging
<p>Stochastic optical reconstruction microscopy (STORM) allows widefield imaging with single-molecule resolution by calculating the coordinates of individual fluorophores from the separation of the fluorophore emission in both time and space. Such separation is achieved by photoswitching the fluorophores between a long-lived OFF state and an emissive ON state. While STORM can image single molecules, molecular counting remains challenging due to undercounting errors from photobleached or overlapping dyes and overcounting artifacts from the repetitive random blinking of the dyes. Here, we show that fluorophores can be switched electrochemically for STORM imaging (EC-STORM), with excellent control over the switching kinetics, duty cycle, and recovery yield. Using EC-STORM, we demonstrate molecular counting by using electrochemical potential to control the photophysics of dyes. The random blinking of dyes is suppressed by a negative potential but the switching ON event can be activated by a short pulsed positive potential, such that the frequency of ON events scales linearly with the number of underlying dyes. We also demonstrate the EC-STORM of tubulins in fixed cells with a spatial resolution as low as ~28 nm and counting of single Alexa 647 fluorophores on various DNA nanoruler structures. This control over fluorophore switching will enable EC-STORM to be broadly applicable in super-resolution imaging and molecular counting.</p>
Source data for: Electrochemically controlled blinking of fluorophores for quantitative STORM imaging
Open the record for dataset details and reuse information.
Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas
<p>Fluorescent dyes used for single-molecule spectroscopy can undergo millions of excitation-emission<br> cycles before photobleaching. Due to the upconcentration of light in a plasmonic hotspot, the<br> conditions for fluorescent dyes are even more demanding inDNAorigami nanoantennas. Here, we<br> briefly review the current state of fluorophore stabilization for single-molecule imaging and reveal<br> additional factors relevant in the context of plasmonic fluorescence enhancement. Weshow that<br> despite the improved photostability of single-molecule fluorophores byDNAorigami nanoantennas,<br> their performance in the intense electric fields in plasmonic hotspots is still limited by the underlying<br> photophysical processes, such as formation of dim states and photoisomerization. These photophysical<br> processes limit the photon count rates, increase heterogeneity and aggravate quantification of<br> fluorescence enhancement factors. These factors also reduce the time resolution that can be achieved<br> in biophysical single-molecule experiments. Finally, we show how the photophysics of aDNAhairpin<br> assay with a fluorophore-quencher pair can be influenced by plasmonicDNAorigami nanoantennas<br> leading to implications for their use in fluorescence-based diagnostic assays. Especially, we show that<br> such assays can produce false positive results by premature photobleaching of the dark quencher. Here we demonstrate the raw data on which our findings based on.</p>
Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking
<p><strong>This upload contains raw data and simulation software underlying the results presented in a manuscript submitted for peer-review</strong><strong>, with the title:</strong></p> <p><strong> </strong></p> <p><strong>Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking</strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p><strong>C Venugopal Srambickal<sup>1,*</sup>, H Esmaeeli<sup>1,*</sup>, J Piguet<sup>1</sup>, L Reinkensmeier<sup>2</sup>, R Siegmund<sup>2</sup>, A Agostinho<sup>3</sup> ,M Bates<sup>2</sup>, A Egner<sup>2</sup>, J Widengren<sup>1,**</sup></strong></p> <p><sup>1</sup> Experimental Biomolecular Physics, Bio-Opto-Nano Unit, Department of Applied Physics, Royal Institute of Technology, SE-10691 Stockholm, Sweden</p> <p><sup>2 </sup>Department of Optical Nanoscopy, Institute for Nanophotonics, D-37077 Göttingen, Germany</p> <p><sup>3</sup> Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, SE-17165 Solna, Sweden</p> <p><sup>*</sup> Contributed equally</p> <p><sup>**</sup> Corresponding author: jwideng@kth.se</p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>MINimal photon FLUXes (MINFLUX) offers super-resolution microscopy (SRM) with nanometer localization precision, with lower fluorophore brightness and photostability requirements than for other SRM techniques. Nonetheless, low localization probabilities have been reported in several MINFLUX studies, and a broader use of less bright and photostable fluorophores, including near-infrared (NIR) fluorophores has been difficult to realize. In this work, we identified fluorophore blinking as a main cause of erroneous (and dismissed) fluorophore localizations in MINFLUX imaging and devised strategies to overcome these effects. We systematically studied the blinking/switching properties of cyanine fluorophores emitting in the far-red or NIR range, over typical time scales (µs-10ms), sample and excitation conditions used in MINFLUX imaging. Subsequent simulations of representative MINFLUX localization procedures showed that trans-cis isomerization, and in particular photo-reduction of the fluorophores, can generate significant localization errors. These localization errors, however, could be suppressed by balanced redox buffers and repetitive excitation beam scans. Implementing these strategies, and replacing the slower, intrinsic switching of the fluorophores needed for the localization by transient binding of fluorophore-labelled DNA strands to complementary DNA strands attached to the targets (DNA-PAINT), we could for the first time demonstrate NIR-MINFLUX imaging with nanometer localization precision. This work presents an overall strategy, where fluorophore blinking characterization and subsequent simulations make it possible to design optimal sample and excitation conditions, opening for NIR-MINFLUX imaging, as well as for a broader use of fluorophores in MINFLUX and related SRM studies.</p> <p>Acknowledgements:</p> <p>This study was supported by the European Union's Horizon 2020 research and innovation program under grant agreement 101017180 (NanoVIB).</p> <p> </p> <p><strong>Files with raw data on which the manuscript is based are grouped into folders according to the figures/tables in the manuscript where the extracted results are presented. Additionally, software developed and used for the simulations are arranged into a separate folder. </strong></p> <p> </p>
Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification: data and code example
<p>Minimal code example, raw and derived data for the publication on 'Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification'.</p>
Detection and Delineation of Necrotizing Fasciitis Via a Vascular Perfusion Fluorophore
ClinicalTrials.gov study NCT04839302. IPD Sharing: NO. Countries: 1. Publications: 3.
Data and code for "Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation"
<p>Representative data and source code for the manuscript "Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation"</p>
Dataset to submitted manuscript "Imaging the blinking properties of a mitochondrial fluorophore marker turns it into a multi-functional sensing probe"
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to Light: Science & Applications, and entitled:</strong></p> <p> </p> <p><strong><em>Imaging the blinking properties of a mitochondrial fluorophore marker turns it into a multi-functional sensing probe</em></strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Zhixue Du<sup>a</sup><em>, </em>Joachim Piguet<sup>a,+</sup>, Gleb Baryshnikov<sup>b,+</sup>, Johan Tornmalm<sup>a</sup>, Baris Demirbay<sup>a</sup>, Hans Ågren<sup>b</sup>, Jerker Widengren<sup>a,*</sup></p> <p> </p> <p><sup>a</sup> Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova Univ Center 106 91 Stockholm, Sweden</p> <p><sup>b</sup> Royal Institute of Technology (KTH), Dept Theroretical Chemistry and Biology, Albanova Univ Center 106 91 Stockholm, Sweden</p> <p><sup>+</sup> Contributed equally</p> <p>* Corresponding author: Email: <a href="mailto:jwideng@kth.se">jwideng@kth.se</a>, Phone: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>By transient state (TRAST) measurements, monitoring the average fluorescence intensity upon excitation modulation, we show that the mitochondrial localization fluorophore 10-Nonyl Acridine Orange (NAO) exhibits prominent singlet-triplet state transitions and can act as a light-induced Lewis acid forming a red-emissive doublet radical. The blinking properties resulting from these transitions can be monitored in a broadly applicable manner, and under biologically relevant conditions. By TRAST studies of NAO in small unilamellar vesicles (SUVs) we show that these blinking properties are highly environment sensitive, specifically reflecting local oxygen concentrations, redox conditions, membrane charge, fluidity and lipid compositions. In SUVs containing the phospholipid cardiolipin (CL) the NAO blinking properties depend not only on the concentration of the CL added, but also on the CL acyl chain composition. The blinking also reflects hydroxyl ion dependent transitions to and from the NAO doublet radical. This makes it possible to monitor local pH and buffering properties, from a 3D bulk buffer above the membrane, or from a 2D buffer at the membrane surface itself. Finally, by live cell TRAST imaging, we show that the fluorescence blinking properties of NAO can also be imaged in a spatially resolved manner, and that this commercially available location-specific fluorophore thereby can be turned into a multi-parametric intracellular sensing probe. This study demonstrates new possibilities for fundamental membrane studies in artificial vesicles and live cells, using existing fluorophore markers, monitoring parameters and conditions of large biological relevance, which are difficult to retrieve by other means.</p>
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