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13 results for “single-molecule FRET”
Super-Resolved FRET Imaging by Confocal Fluorescence-Lifetime Single-Molecule Localization Microscopy
<p>FRET-based methods are a special tool for detecting interactions between (bio)molecules and their immediate environment. The spatial distribution of molecular interactions and functional states can be seen using FLIM (Fluorescence Lifetime IMaging) and FRET imaging. The spatial information, accuracy, and dynamic range of the observed signals are, however, constrained by the fact that conventional FLIM and FRET imaging only provides average information over an ensemble of molecules within a diffraction-limited volume. On the other hand, conventional Single Molecule Localization Microscopy (SMLM) relies on highly sensitive multi-pixel detectors (e.g. sCMOS or EM-CCD) whose time resolution is not suitable for fluorescence lifetime measurements.</p> <p>Here, we demonstrate a method for obtaining super-resolved FRET imaging using confocal fluorescence-lifetime single-molecule localization microscopy. The proof of concept was carried out using a DNA origami sample for performing DNA-PAINT measurements in combination with fluorogenic probes for reducing background signal. With this method, We show that FRET events separated by sub-diffraction distances can be distinguished based on lifetime modifications.</p>
Dynamic FRET example videos related to "Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages"
<p>Videos of dynamic switching between iso-I and iso-II conformations of a holiday junction at 50 mM Magnesium resulting in high and low FRET from Cy3 and Alexa647 labels positioned on the arms. Holiday junctions are surface immobilized through a biotin attachment and imaged using TIRF microscopy. The camera sensor is split using a dual view so that the acceptor emission is on the top and the donor emission is on the bottom. Videos from each position are provided as compressed zip files containing a sequence of tif files and associated metadata text file. Image sequences were collected using Micro-Manager 2.0 using ALEX or alternating laser excitation with alternating 637 and 532 pulses separated as two different channels. Beam profile images are provided for 637 and 532 excitation allowing for correction of the non-uniform beam profiles. The following 2D affine transformation matrix can be used to transform from the top acceptor emission region to the bottom donor emission region during processing.</p> <p>Affine 2D transformation from top to bottom: (m00, m01, m02, m10, m11, m12), (1.00276, 0.000208, 1.01236, 0.000267, 1.00312, 507.21025)</p> <p>A detailed image processing workflow for this dataset using Mars can be found under the example section at <a href="https://duderstadt-lab.github.io/mars-docs/">https://duderstadt-lab.github.io/mars-docs/</a> or directly at <a href="https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/">https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/</a></p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def
<p>smTIRF-FRET Data for Fig 2, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde
<p>smTIRF-FRET Data for Fig 7, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 1df
<p>smTIRF-FRET Data for Fig 1, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Datasets for "Precision and accuracy of single-molecule FRET measurements – a multi-laboratory benchmark study"
<p>Supplementary material (raw data) for Fig. 2 in "<strong>Precision and accuracy of single-molecule FRET measurements – a multi-laboratory benchmark study</strong>" to be published with Nature Methods</p> <p>The confocal data is given in ht3 and hdf5 format.</p> <p>For the TIRF data the original TIFF-stacks are uploaded including the calibration files.</p>
Can DyeCycling break the photobleaching limit in single-molecule FRET?
<p><strong>Abstract. </strong>Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a prohibitively narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce <em>‘DyeCycling’</em>, a measurement scheme with which we aim to break the photobleaching limit in single-molecule FRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide >100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.</p>
Data deposition for "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins"
<p>The deposited data for the publication "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins".</p> <p>Data contains folder and sub-folders for the raw data, Main excel sheet named as "MasterTable_FRET-Challenge-Protein-Dynamics_Nat_Meth_Agam et al" has most of the data used in the publication. Another excel sheets "Data List for FIgures for Agam et al_revised" and "Data List for Supplmentary FIgures for Agam et al_revised" have the information regarding the Figure-wise data description and where the respective data locates.</p>
Data from: Quantitative single-molecule FLIM and PIE-FRET imaging of biomolecular systems
Open the record for dataset details and reuse information.
Single-Molecule FRET-Resolved Protein Dynamics - from Plasmid to Data in Six Steps
<p>SmFRET trace files of 58 yeast Hsp90 molecules (in presence of AMP-PNP) containing raw intensity values through time of acceptor emission after acceptor excitation (r_r_*), donor emission after donor excitation (o_g_*), and acceptor emission after donor excitation (r_g_*).</p>
Data from "Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels"
<p>Source data for all figures; full table of all nucleic acid sequences used; Supplementary Video 1 showing rotating view of Fig. 4e.</p>
Single-molecule two- and three-colour FRET studies reveal a hidden transition state in SNARE disassembly by NSF
<p>Raw Data for the NC manuscript</p>
Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET
<p>Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modeling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.</p>
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