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Journal articles on the topic 'FRET experiments'

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Author: Grafiati

Published: 6 September 2023

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1

Kong, Xiangxu, Eyal Nir, Kambiz Hamadani, and Shimon Weiss. "Photobleaching Pathways in Single-Molecule FRET Experiments." Journal of the American Chemical Society 129, no. 15 (April 2007): 4643–54. http://dx.doi.org/10.1021/ja068002s.

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2

Skruzny, Pohl, and Abella. "FRET Microscopy in Yeast." Biosensors 9, no. 4 (October 11, 2019): 122. http://dx.doi.org/10.3390/bios9040122.

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Förster resonance energy transfer (FRET) microscopy is a powerful fluorescence microscopy method to study the nanoscale organization of multiprotein assemblies in vivo. Moreover, many biochemical and biophysical processes can be followed by employing sophisticated FRET biosensors directly in living cells. Here, we summarize existing FRET experiments and biosensors applied in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, two important models of fundamental biomedical research and efficient platforms for analyses of bioactive molecules. We aim to provide a practical guide on suitable FRET techniques, fluorescent proteins, and experimental setups available for successful FRET experiments in yeasts.

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3

Chirio-Lebrun, Maria-Chantal, and Michel Prats. "Fluorescence resonance energy transfer (FRET): theory and experiments." Biochemical Education 26, no. 4 (October 1998): 320–23. http://dx.doi.org/10.1016/s0307-4412(98)80010-1.

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4

Buning, Ruth, and John van Noort. "Single-pair FRET experiments on nucleosome conformational dynamics." Biochimie 92, no. 12 (December 2010): 1729–40. http://dx.doi.org/10.1016/j.biochi.2010.08.010.

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5

Hohng, Sungchul, Sanghwa Lee, Jinwoo Lee, and Myung Hyun Jo. "Maximizing information content of single-molecule FRET experiments: multi-color FRET and FRET combined with force or torque." Chem. Soc. Rev. 43, no. 4 (2014): 1007–13. http://dx.doi.org/10.1039/c3cs60184f.

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6

Barth, Anders, Oleg Opanasyuk, Thomas-Otavio Peulen, Suren Felekyan, Stanislav Kalinin, Hugo Sanabria, and Claus A. M. Seidel. "Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines." Journal of Chemical Physics 156, no. 14 (April 14, 2022): 141501. http://dx.doi.org/10.1063/5.0089134.

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Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E–τ D diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.

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7

Hartmann, Andreas, Frederic Berndt, Simon Ollmann, Georg Krainer, and Michael Schlierf. "In situ temperature monitoring in single-molecule FRET experiments." Journal of Chemical Physics 148, no. 12 (March 28, 2018): 123330. http://dx.doi.org/10.1063/1.5008966.

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8

Weiss, A., N. Melamed-Book, O. Avital, and M. Brandeis. "A Mixed Cell Protocol for Sensitized Emission FRET Experiments." Microscopy and Microanalysis 12, S02 (July 31, 2006): 434–35. http://dx.doi.org/10.1017/s1431927606062556.

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9

Schröder, G. F., and H. Grubmüller. "FRETsg: Biomolecular structure model building from multiple FRET experiments." Computer Physics Communications 158, no. 3 (April 2004): 150–57. http://dx.doi.org/10.1016/j.cpc.2004.02.001.

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10

Hanke, Christian A., Mykola Dimura, Thomas-Otavio Peulen, Holger Gohlke, and Claus A. M. Seidel. "Integrative Molecular Modelling of Biomolecules Guided by FRET Experiments." Biophysical Journal 114, no. 3 (February 2018): 681a. http://dx.doi.org/10.1016/j.bpj.2017.11.3673.

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11

Hohng, Sungchul, Sanghwa Lee, Jinwoo Lee, and Myung Hyun Jo. "ChemInform Abstract: Maximizing Information Content of Single-Molecule FRET Experiments: Multi-Color FRET and FRET Combined with Force or Torque." ChemInform 45, no. 15 (March 27, 2014): no. http://dx.doi.org/10.1002/chin.201415281.

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12

Hippe, Laura, Šimons Svirskis, Modra Murovska, and Mārtiņš Kālis. "Optimisation of Widefield Fluorescence Fret System for Studying Separate Molecule Interactions." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. 72, no. 4 (August 1, 2018): 252–58. http://dx.doi.org/10.2478/prolas-2018-0065.

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Abstract The Förster Resonance Energy Transfer (FRET) method has wide application in modern science for studying protein–protein interactions and conformational changes. FRET allows to assess molecular interactions by measuring energy transfer between acceptor and donor fluorophores coupled to the molecule(s) of interest. The method demands high precision in experimental design, experimental settings and correct data interpretation. Therefore, we tested several parameters to estimate FRET measurement accuracy in our Nikon wide-field fluorescence FRET system. The experiments were performed in a HEK-293 cell line transfected with DNA constructs expressing Calcium Release-Activated Channel (CRAC) subunits STIM1 and ORAI1 coupled to donor fluorophore Cyan Fluorescent Protein (CFP) and acceptor fluorophore Yellow Fluorescent Protein (YFP), respectively. Exposure time and approach of data analysis varied throughout experiments in order to optimise FRET data quality. Dependence of FRETeff values on measurement quality and donor/acceptor fluorophore ratio in the cells was estimated. We demonstrated that, using the wide-field fluorescence FRET system, minimising the exposure of fluorophores before measurement using neutral density (ND) filters considerably minimises undesirable photo-bleaching of the fluorophores. There was a strong correlation between the CFP/YFP ratio in the cells and the observed FRET level, suggesting that only cells with certain donor/acceptor ratio might be comparable. We also showed impact of FRET measurement quality, defined as accordance of FRET pixels to Gaussian distribution, on FRET artefacts. Knowledge obtained during our experiments may be important for approbating similar wide-field fluorescence FRET systems to study two separate molecule interactions and for understanding the correct setup of the experiments and data interpretation.

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13

Gavrikov, Alexey S., Nina G. Bozhanova, Mikhail S. Baranov, and Alexander S. Mishin. "Add and Go: FRET Acceptor for Live-Cell Measurements Modulated by Externally Provided Ligand." International Journal of Molecular Sciences 23, no. 8 (April 15, 2022): 4396. http://dx.doi.org/10.3390/ijms23084396.

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A substantial number of genetically encoded fluorescent sensors rely on the changes in FRET efficiency between fluorescent cores, measured in ratiometric mode, with acceptor photobleaching or by changes in fluorescence lifetime. We report on a modulated FRET acceptor allowing for simplified one-channel FRET measurement based on a previously reported fluorogen-activating protein, DiB1. Upon the addition of the cell-permeable chromophore, the fluorescence of the donor-fluorescent protein mNeonGreen decreases, allowing for a simplified one-channel FRET measurement. The reported chemically modulated FRET acceptor is compatible with live-cell experiments and allows for prolonged time-lapse experiments with dynamic energy transfer evaluation.

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14

Nettels, Daniel, Dominik Haenni, Sacha Maillot, Moussa Gueye, Anders Barth, Verena Hirschfeld, Christian G. Hübner, Jérémie Léonard, and Benjamin Schuler. "Excited-state annihilation reduces power dependence of single-molecule FRET experiments." Physical Chemistry Chemical Physics 17, no. 48 (2015): 32304–15. http://dx.doi.org/10.1039/c5cp05321h.

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15

Heinrich, Philippe, Mariano Gonzalez Pisfil, Jonas Kahn, Laurent Héliot, and Aymeric Leray. "Implementation of Transportation Distance for Analyzing FLIM and FRET Experiments." Bulletin of Mathematical Biology 76, no. 10 (September 25, 2014): 2596–626. http://dx.doi.org/10.1007/s11538-014-0025-9.

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16

Kulesza, Alexander, Steven Daly, and Philippe Dugourd. "Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-β12–28linked to FRET experiments." Physical Chemistry Chemical Physics 19, no. 14 (2017): 9470–77. http://dx.doi.org/10.1039/c7cp00611j.

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The free energy landscapes of Aβ-peptide dimer models under different prototype conditions support the hypothesis that the gas-phase action-FRET measurement after electrospray ionization operates under non-equilibrium conditions, with a memory of the solution conditions – even for the dimer of this relatively short peptide.

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17

Pantano, Sergio, Alessandro Marcello, Arianna Sabò, Aldo Ferrari, Vittorio Pellegrini, Fabio Beltram, Mauro Giacca, and Paolo Carloni. "A Model of N-Terminal Cyclin T1 Based on FRET Experiments." Journal of Theoretical Medicine 6, no. 2 (2005): 73–79. http://dx.doi.org/10.1080/10273660500149430.

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Human Cyclin T1 is the cyclin partner of kinase CDK9 in the positive transcription elongation factor b (P-TEFb). P-TEFb is recruited by Tat, the transactivator of the human immunodeficiency virus type 1 (HIV-1), to the viral promoter by direct interactions between Tat, Cyclin T1 and thecis-acting transactivation-responsive region (TAR) present at the 5′-end of each viral mRNA. At present, no structural data for Cyclin T1 are available. Here, we build a structural model of an N-terminus portion of Cyclin T1 (aa 27–263) based on the X-ray structure of Cyclin H. The model is compared with site directed mutagenesis data from the literature and validated by fluorescence resonance energy transfer (FRET) using Tat as a probe in living cells. This model provides a first step towards the structural characterization of the CDK9–CycT1–Tat-TAR complex, which is crucial for HIV-1 replication and may constitute a promising target for pharmaceutical intervention.

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18

King, Christopher, Sarvenaz Sarabipour, Patrick Byrne, Daniel J. Leahy, and Kalina Hristova. "The FRET Signatures of Noninteracting Proteins in Membranes: Simulations and Experiments." Biophysical Journal 106, no. 6 (March 2014): 1309–17. http://dx.doi.org/10.1016/j.bpj.2014.01.039.

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19

Best, Robert B., Wenwei Zheng, Alessandro Borgia, Karin Buholzer, Madeleine B. Borgia, Hagen Hofmann, Andrea Soranno, et al. "Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”." Science 361, no. 6405 (August 30, 2018): eaar7101. http://dx.doi.org/10.1126/science.aar7101.

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Riback et al. (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no “contradiction” between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.

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20

Levy, Shiri, Christian D. Wilms, Eliaz Brumer, Joy Kahn, Lilach Pnueli, Yoav Arava, Jens Eilers, and Daniel Gitler. "SpRET: Highly Sensitive and Reliable Spectral Measurement of Absolute FRET Efficiency." Microscopy and Microanalysis 17, no. 2 (February 21, 2011): 176–90. http://dx.doi.org/10.1017/s1431927610094493.

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AbstractContemporary research aims to understand biological processes not only by identifying participating proteins, but also by characterizing the dynamics of their interactions. Because Förster's Resonance Energy Transfer (FRET) is invaluable for the latter undertaking, its usage is steadily increasing. However, FRET measurements are notoriously error-prone, especially when its inherent efficiency is low, a not uncommon situation. Furthermore, many FRET methods are either difficult to implement, are not appropriate for observation of cellular dynamics, or report instrument-specific indices that hamper communication of results within the scientific community. We present here a novel comprehensive spectral methodology, SpRET, which substantially increases both the reliability and sensitivity of FRET microscopy, even under unfavorable conditions such as weak fluorescence or the presence of noise. While SpRET overcomes common pitfalls such as interchannel crosstalk and direct excitation of the acceptor, it also excels in removal of autofluorescence or background contaminations and in correcting chromatic aberrations, often overlooked factors that severely undermine FRET experiments. Finally, SpRET quantitatively reports absolute rather than relative FRET efficiency values, as well as the acceptor-to-donor molar ratio, which is critical for full and proper interpretation of FRET experiments. Thus, SpRET serves as an advanced, improved, and powerful tool in the cell biologist's toolbox.

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21

Sekatskii, S. K., K. Dukenbayev, M. Mensi, A. G. Mikhaylov, E. Rostova, A. Smirnov, N. Suriyamurthy, and G. Dietler. "Single molecule fluorescence resonance energy transfer scanning near-field optical microscopy: potentials and challenges." Faraday Discussions 184 (2015): 51–69. http://dx.doi.org/10.1039/c5fd00097a.

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A few years ago, single molecule Fluorescence Resonance Energy Transfer Scanning Near-Field Optical Microscope (FRET SNOM) images were demonstrated using CdSe semiconductor nanocrystal–dye molecules as donor–acceptor pairs. Corresponding experiments reveal the necessity to exploit much more photostable fluorescent centers for such an imaging technique to become a practically used tool. Here we report the results of our experiments attempting to use nitrogen vacancy (NV) color centers in nanodiamond (ND) crystals, which are claimed to be extremely photostable, for FRET SNOM. All attempts were unsuccessful, and as a plausible explanation we propose the absence (instability) of NV centers lying close enough to the ND border. We also report improvements in SNOM construction that are necessary for single molecule FRET SNOM imaging. In particular, we present the first topographical images of single strand DNA molecules obtained with fiber-based SNOM. The prospects of using rare earth ions in crystals, which are known to be extremely photostable, for single molecule FRET SNOM at room temperature and quantum informatics at liquid helium temperatures, where FRET is a coherent process, are also discussed.

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22

Klejevskaja, Beata, Alice L. B. Pyne, Matthew Reynolds, Arun Shivalingam, Richard Thorogate, Bart W. Hoogenboom, Liming Ying, and Ramon Vilar. "Studies of G-quadruplexes formed within self-assembled DNA mini-circles." Chemical Communications 52, no. 84 (2016): 12454–57. http://dx.doi.org/10.1039/c6cc07110d.

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We have developed self-assembled DNA mini-circles that contain a G-quadruplex-forming sequence and demonstrate by FRET that the G-quadruplex unfolding kinetics are 10-fold slower than for the simpler 24-mer G-quadruplex that is commonly used for FRET experiments.

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23

Huynh, Khon C., Volker R. Stoldt, Marianna Gyenes, Abdelouahid El-Khattouti, and Rudiger E. Scharf. "Fibronectin Unfolding by Platelets and Its Effect on Platelet Adhesion and Aggregation." Blood 118, no. 21 (November 18, 2011): 2209. http://dx.doi.org/10.1182/blood.v118.21.2209.2209.

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Abstract Abstract 2209 Introduction: Fibronectin (Fn), a dimeric adhesive glycoprotein of 230 to 250 kDa monomers, is present both in plasma and the extracellular matrix. Fn has been suggested to interact with platelets, subsequently being unfolded and forming fibrillar-like networks that contribute to platelet adhesion and aggregation. In our study, we examined the effect of Fn isolated from plasma on platelet adhesion and aggregation in vitro. Specifically, we explored the effect of Fn unfolding while interacting with platelets. Methods: For adhesion experiments, mepacrine-labeled washed platelets in the absence or presence of exogenous Fn (100 μg/ml) were incubated in wells pre-coated with collagen type I, fibrinogen (Fg) or Fn (10 μg/ml each) for 30 min at 37°C. For aggregation experiments, washed platelets were stimulated with 40 nM PMA or 10 μg/ml collagen in the absence or presence of Fn (300 μg/ml). For fluorescence resonance energy transfer (FRET) experiments, Fn isolated from human plasma was doubly conjugated with alexa fluor 488 and 546. Labeled Fn was mixed with 10-fold excess of unlabeled Fn to prevent energy transfer between adjacent protein molecules. Fn mixtures (20 or 100 μg/ml) were incubated for 3 h at 22°C with washed platelets in suspension (108/ml) or with platelets adherent onto immobilized Fn (50 μg/ml). In both settings, platelets were stimulated by 40 nM PMA. In some experiments, platelets were pre-incubated with the monoclonal antibodies LM609 or 10E5 (10 μg/ml) to block αvβ3 or αIIbβ3, respectively, prior to the addition of labeled Fn. For control, FRET signals of Fn mixtures without platelets were recorded. Results: Upon addition of soluble Fn (100 μg/ml) to washed platelets and subsequent co-incubation in wells pre-coated with collagen, Fg, or Fn (10 μg/ml) for 30 min, the percentage (mean % ± SD) of platelets adherent onto one of the immobilized ligands increased significantly by 228±33 (p=0.0112, n=3), 249±42 (p=0.005, n=3), or 198±21 (p=0.0017, n=3), respectively, as compared to adhesion experiments without addition of soluble Fn. By contrast, Fn had an opposing effect on platelet aggregation. Thus, addition of Fn (300 μg/ml) to washed platelets resulted in a reduction of 25 % or 50 % in platelet aggregation induced by PMA (40nM) or collagen (10 μg/ml), respectively. To determine Fn unfolding, the protein was doubly labeled with alexa fluor 488 (donor) randomly at 7–9 amine residues and alexa fluor 546 (acceptor) specifically at 4 free cysteine residues for FRET analyses. To access the sensitivity of FRET for conformational changes in Fn, we exposed labeled Fn to increasing concentrations of GdnHCl (1–4 M) and measured FRET. FRET signals, defined by the ratio of acceptor to donor fluoresecence intensity, varied over the range of GdnHCl concentrations indicating the conformational changes in Fn from its compact to its unfolded state. Fn in its compact conformation (0 M GdnHCl) had a FRET signal of 0.55 (100%) which decreased to 0.34 (63%), as Fn extended in 1 M GdnHCl solution. Further unfolding of Fn in 2 M, 3M and 4 M GdnHCl reduced the FRET signal to 0.27 (50%), 0.23 (44%) and 0.21 (39%), respectively. Addition of labeled Fn to PMA-activated platelets adherent onto immobilized unlabled Fn caused a slow but progressive decrease in FRET signal by 4% at 1 h, 5 % at 2 h and 6% at 3 h incubation. The decrease in FRET signal was reduced to 2% when platelet αvβ3 was blocked by LM609. By contrast, FRET remained unchanged in control experiments without platelets. The same was true when labeled Fn was incubated with PMA-activated platelets in suspension or in the presence of 10E5 (blocking αIIbβ3). Conclusion: Our in vitro studies strongly suggest that fibronectin can play a dual role in hemostasis by promoting platelet adhesion onto immobilized ligands but reducing platelet aggregation. We also demonstrate that activated adherent but not suspended platelets can indeed progressively unfold fibronectin, thereby inducing profound conformational changes that may explain its oppositional effects in platelet adhesion and aggregation. Moreover, our data suggest that unfolding of fibronectin caused by adherent platelets is governed by β3 integrins. Hereby, αIIbβ3 plays a predominant role in comparison to αvβ3. Disclosures: No relevant conflicts of interest to declare.

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24

Reddy, Gopireddy Raghavender, Toni M. West, Zhong Jian, Mark Jaradeh, Qian Shi, Ying Wang, Ye Chen-Izu, and Yang K. Xiang. "Illuminating cell signaling with genetically encoded FRET biosensors in adult mouse cardiomyocytes." Journal of General Physiology 150, no. 11 (September 21, 2018): 1567–82. http://dx.doi.org/10.1085/jgp.201812119.

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FRET-based biosensor experiments in adult cardiomyocytes are a powerful way of dissecting the spatiotemporal dynamics of the complicated signaling networks that regulate cardiac health and disease. However, although much information has been gleaned from FRET studies on cardiomyocytes from larger species, experiments on adult cardiomyocytes from mice have been difficult at best. Thus the large variety of genetic mouse models cannot be easily used for this type of study. Here we develop cell culture conditions for adult mouse cardiomyocytes that permit robust expression of adenoviral FRET biosensors and reproducible FRET experimentation. We find that addition of 6.25 µM blebbistatin or 20 µM (S)-nitro-blebbistatin to a minimal essential medium containing 10 mM HEPES and 0.2% BSA maintains morphology of cardiomyocytes from physiological, pathological, and transgenic mouse models for up to 50 h after adenoviral infection. This provides a 10–15-h time window to perform reproducible FRET readings using a variety of CFP/YFP sensors between 30 and 50 h postinfection. The culture is applicable to cardiomyocytes isolated from transgenic mouse models as well as models with cardiac diseases. Therefore, this study helps scientists to disentangle complicated signaling networks important in health and disease of cardiomyocytes.

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25

Nir, Eyal, Xavier Michalet, Kambiz M. Hamadani, Ted A. Laurence, Daniel Neuhauser, Yevgeniy Kovchegov, and Shimon Weiss. "Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments†." Journal of Physical Chemistry B 110, no. 44 (November 2006): 22103–24. http://dx.doi.org/10.1021/jp063483n.

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26

Turshatov, Andrey, and Jörg Adams. "A new monomeric FRET-acceptor for polymer interdiffusion experiments on polymer dispersions." Polymer 48, no. 26 (December 2007): 7444–48. http://dx.doi.org/10.1016/j.polymer.2007.10.023.

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27

Krainer, Georg, Andreas Hartmann, and Michael Schlierf. "farFRET: Extending the Range in Single-Molecule FRET Experiments beyond 10 nm." Nano Letters 15, no. 9 (June 26, 2015): 5826–29. http://dx.doi.org/10.1021/acs.nanolett.5b01878.

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28

Chung, Hoi Sung, John M. Louis, and William A. Eaton. "Distinguishing between Protein Dynamics and Dye Photophysics in Single-Molecule FRET Experiments." Biophysical Journal 98, no. 4 (February 2010): 696–706. http://dx.doi.org/10.1016/j.bpj.2009.12.4322.

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29

Torella, Joseph P., Seamus J. Holden, Yusdi Santoso, Johannes Hohlbein, and Achillefs N. Kapanidis. "Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis." Biophysical Journal 100, no. 6 (March 2011): 1568–77. http://dx.doi.org/10.1016/j.bpj.2011.01.066.

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30

Best, Robert B., Hagen Hofmann, Daniel Nettels, and Benjamin Schuler. "Quantitative Interpretation of FRET Experiments via Molecular Simulation: Force Field and Validation." Biophysical Journal 108, no. 11 (June 2015): 2721–31. http://dx.doi.org/10.1016/j.bpj.2015.04.038.

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Krainer, Georg, Andreas Hartmann, and Michael Schlierf. "farFRET: Extending the Range in Single-Molecule FRET Experiments Beyond 10 nm." Biophysical Journal 110, no. 3 (February 2016): 195a. http://dx.doi.org/10.1016/j.bpj.2015.11.1085.

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32

Yoo, Jejoong, Hajin Kim, Taekjip Ha, and Aleksei Aksimentiev. "Effector-Free Molecular Mechanism of Epigenetic Regulation Revealed by Molecular Dynamics Simulations and Single-Molecule FRET Experiments." Biophysical Journal 110, no. 3 (February 2016): 561a—562a. http://dx.doi.org/10.1016/j.bpj.2015.11.3003.

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33

Markwardt, Michele L., Gert-Jan Kremers, Catherine A. Kraft, Krishanu Ray, Paula J. C. Cranfill, Korey A. Wilson, Richard N. Day, Rebekka M. Wachter, Michael W. Davidson, and Megan A. Rizzo. "An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching." PLoS ONE 6, no. 3 (March 29, 2011): e17896. http://dx.doi.org/10.1371/journal.pone.0017896.

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Cyan fluorescent proteins (CFPs), such as Cerulean, are widely used as donor fluorophores in Förster resonance energy transfer (FRET) experiments. Nonetheless, the most widely used variants suffer from drawbacks that include low quantum yields and unstable flurorescence. To improve the fluorescence properties of Cerulean, we used the X-ray structure to rationally target specific amino acids for optimization by site-directed mutagenesis. Optimization of residues in strands 7 and 8 of the β-barrel improved the quantum yield of Cerulean from 0.48 to 0.60. Further optimization by incorporating the wild-type T65S mutation in the chromophore improved the quantum yield to 0.87. This variant, mCerulean3, is 20% brighter and shows greatly reduced fluorescence photoswitching behavior compared to the recently described mTurquoise fluorescent protein in vitro and in living cells. The fluorescence lifetime of mCerulean3 also fits to a single exponential time constant, making mCerulean3 a suitable choice for fluorescence lifetime microscopy experiments. Furthermore, inclusion of mCerulean3 in a fusion protein with mVenus produced FRET ratios with less variance than mTurquoise-containing fusions in living cells. Thus, mCerulean3 is a bright, photostable cyan fluorescent protein which possesses several characteristics that are highly desirable for FRET experiments.

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34

Riback, Joshua A., Micayla A. Bowman, Adam Zmyslowski, Catherine R. Knoverek, John Jumper, Emily B. Kaye, Karl F. Freed, Patricia L. Clark, and Tobin R. Sosnick. "Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”." Science 361, no. 6405 (August 30, 2018): eaar7949. http://dx.doi.org/10.1126/science.aar7949.

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Best et al. claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al. comment. A plausible origin is fluorophore interactions in FRET experiments.

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35

Walczewska-Szewc, Katarzyna, and Ben Corry. "Do bifunctional labels solve the problem of dye diffusion in FRET analysis?" Phys. Chem. Chem. Phys. 16, no. 35 (2014): 18949–54. http://dx.doi.org/10.1039/c4cp02110j.

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36

Yahia-Ammar, Akram, Aline M. Nonat, Anne Boos, Jean-Luc Rehspringer, Zouhair Asfari, and Loïc J. Charbonnière. "Thin-coated water soluble CdTeS alloyed quantum dots as energy donors for highly efficient FRET." Dalton Trans. 43, no. 41 (2014): 15583–92. http://dx.doi.org/10.1039/c4dt01502a.

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37

Muraru, Sorin, Sebastian Muraru, Florentin Romeo Nitu, and Mariana Ionita. "Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods." Journal of Chemical Information and Modeling 62, no. 2 (January 11, 2022): 232–39. http://dx.doi.org/10.1021/acs.jcim.1c00957.

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38

Valentin, Guillaume, Céline Verheggen, Tristan Piolot, Henry Neel, Maïté Coppey-Moisan, and Edouard Bertrand. "Photoconversion of YFP into a CFP-like species during acceptor photobleaching FRET experiments." Nature Methods 2, no. 11 (November 2005): 801. http://dx.doi.org/10.1038/nmeth1105-801.

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van de Meent, Jan-Willem, Jonathan E. Bronson, Chris H. Wiggins, and Ruben L. Gonzalez. "Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments." Biophysical Journal 106, no. 6 (March 2014): 1327–37. http://dx.doi.org/10.1016/j.bpj.2013.12.055.

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Tomov, Toma E., Roman Tsukanov, Rula Masoud, Miran Liber, Noa Plavner, and Eyal Nir. "Disentangling Subpopulations in Single-Molecule FRET and ALEX Experiments with Photon Distribution Analysis." Biophysical Journal 102, no. 5 (March 2012): 1163–73. http://dx.doi.org/10.1016/j.bpj.2011.11.4025.

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41

Rieger, Robert, Andrei Kobitski, Hendrik Sielaff, and G. Ulrich Nienhaus. "Evidence of a Folding Intermediate in RNase H from Single‐Molecule FRET Experiments." ChemPhysChem 12, no. 3 (November 9, 2010): 627–33. http://dx.doi.org/10.1002/cphc.201000693.

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42

Sanz-Paz, Maria, Jerome Wenger, Niek F. van Hulst, Mathieu Mivelle, and Maria F. Garcia-Parajo. "Nanoscale control of single molecule Förster resonance energy transfer by a scanning photonic nanoantenna." Nanophotonics 9, no. 12 (June 29, 2020): 4021–31. http://dx.doi.org/10.1515/nanoph-2020-0221.

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AbstractFörster Resonance Energy Transfer (FRET) is a widely applied technique in biology to accurately measure intra- and inter-molecular interactions at the nanometre scale. FRET is based on near-field energy transfer from an excited donor to a ground state acceptor emitter. Photonic nanoantennas have been shown to modify the rate, efficiency and extent of FRET, a process that is highly dependent on the near-field gradient of the antenna field as felt by the emitters, and thus, on their relative distance. However, most of the experiments reported to date focus on fixed antennas where the emitters are either immobilized or diffusing in solution, so that the distance between the antenna and the emitters cannot be manipulated. Here, we use scanning photonic nanoantenna probes to directly modulate the FRET efficiency between individual FRET pairs with an unprecedented nanometric lateral precision of 2 nm on the antenna position. We find that the antenna acts as an independent acceptor element, competing with the FRET pair acceptor. We directly map the competition between FRET and donor-antenna transfer as a function of the relative position between the antenna and the FRET donor-acceptor pair. The experimental data are well-described by FDTD simulations, confirming that the modulation of FRET efficiency is due to the spatially dependent coupling of the single FRET pair to the photonic antenna.

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Gertler, Arieh, Eva Biener, Krishnan V. Ramanujan, Jean Djiane, and Brian Herman. "Fluorescence resonance energy transfer (FRET) microscopy in living cells as a novel tool for the study of cytokine action." Journal of Dairy Research 72, S1 (July 28, 2005): 14–19. http://dx.doi.org/10.1017/s0022029905001123.

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Fluorescence resonance energy transfer (FRET) microscopy was used to study interactions between proteins in intact cells. We showed that growth hormone (GH) causes transient homodimerization of GH receptors tagged with yellow or cyan fluorescent proteins. The peak of FRET signaling occurred 2 to 4 min after hormonal stimulation and was followed by a decrease in FRET signal. Repeating those experiments in cells pretreated with the inhibitor of internalization methyl-β-cyclodextrin, or in potassium-depleted cells showed no difference in the kinetics of FRET signaling as compared with the non-treated cells, indicating that the decrease in FRET signal does not result from receptor internalization by the pathways inhibited by methyl-β-cyclodextrin or potassium depleted but might occur by other pathways of internalization. Using a similar methodology, we also demonstrated that ovine placental lactogen (oPL) causes transient heterodimerization of GH and prolactin (PRL) receptors 2·5 to 3 min after oPL application. On the other hand, oGH or oPRL had no effect at all, further substantiating the finding the oPL, which lacks a specific receptor, acts in homologous systems by heterodimerization of GH and PRL receptors. We also demonstrated that both PRL and leptin (LEP) are capable of transactivation of the oncogenic receptors erbB2 and erbB3. Upon PRL or LEP stimulation of HEK-293T cells transfected with LEP or PRL receptors and erbB2 or erbB3, erbB proteins are first phosphorylated and then activate MAPK (erk1/erk2). However, the FRET experiments failed to document any evidence of a direct interaction between erbB2 and the PRL or LEP receptors, suggesting that erbB activation probably occurs via activated JAK2, translocated from the respective receptors to erbB2.

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Hogue, Ian B., Adam Hoppe, and Akira Ono. "Quantitative Fluorescence Resonance Energy Transfer Microscopy Analysis of the Human Immunodeficiency Virus Type 1 Gag-Gag Interaction: Relative Contributions of the CA and NC Domains and Membrane Binding." Journal of Virology 83, no. 14 (April 29, 2009): 7322–36. http://dx.doi.org/10.1128/jvi.02545-08.

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ABSTRACT The human immunodeficiency virus type 1 structural polyprotein Pr55Gag is necessary and sufficient for the assembly of virus-like particles on cellular membranes. Previous studies demonstrated the importance of the capsid C-terminal domain (CA-CTD), nucleocapsid (NC), and membrane association in Gag-Gag interactions, but the relationships between these factors remain unclear. In this study, we systematically altered the CA-CTD, NC, and the ability to bind membrane to determine the relative contributions of, and interplay between, these factors. To directly measure Gag-Gag interactions, we utilized chimeric Gag-fluorescent protein fusion constructs and a fluorescence resonance energy transfer (FRET) stoichiometry method. We found that the CA-CTD is essential for Gag-Gag interactions at the plasma membrane, as the disruption of the CA-CTD has severe impacts on FRET. Data from experiments in which wild-type (WT) and CA-CTD mutant Gag molecules are coexpressed support the idea that the CA-CTD dimerization interface consists of two reciprocal interactions. Mutations in NC have less-severe impacts on FRET between normally myristoylated Gag proteins than do CA-CTD mutations. Notably, when nonmyristoylated Gag interacts with WT Gag, NC is essential for FRET despite the presence of the CA-CTD. In contrast, constitutively enhanced membrane binding eliminates the need for NC to produce a WT level of FRET. These results from cell-based experiments suggest a model in which both membrane binding and NC-RNA interactions serve similar scaffolding functions so that one can functionally compensate for a defect in the other.

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Ingram, Justin, Chunfeng Zhang, John R. Cressman, Anupam Hazra, Yina Wei, Yong-Eun Koo, Jokūbas Žiburkus, Raoul Kopelman, Jian Xu, and Steven J. Schiff. "Oxygen and seizure dynamics: I. Experiments." Journal of Neurophysiology 112, no. 2 (July 15, 2014): 205–12. http://dx.doi.org/10.1152/jn.00540.2013.

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We utilized a novel ratiometric nanoquantum dot fluorescence resonance energy transfer (NQD-FRET) optical sensor to quantitatively measure oxygen dynamics from single cell microdomains during hypoxic episodes as well as during 4-aminopyridine (4-AP)-induced spontaneous seizure-like events in rat hippocampal slices. Coupling oxygen sensing with electrical recordings, we found the greatest reduction in the O2 concentration ([O2]) in the densely packed cell body stratum (st.) pyramidale layer of the CA1 and differential layer-specific O2 dynamics between the st. pyramidale and st. oriens layers. These hypoxic decrements occurred up to several seconds before seizure onset could be electrically measured extracellularly. Without 4-AP, we quantified a narrow range of [O2], similar to the endogenous hypoxia found before epileptiform activity, which permits a quiescent network to enter into a seizure-like state. We demonstrated layer-specific patterns of O2 utilization accompanying layer-specific neuronal interplay in seizure. None of the oxygen overshoot artifacts seen with polarographic measurement techniques were observed. We therefore conclude that endogenously generated hypoxia may be more than just a consequence of increased cellular excitability but an influential and critical factor for orchestrating network dynamics associated with epileptiform activity.

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Hu, Ping, and Nicola Tirelli. "Inter-micellar dynamics in block copolymer micelles: FRET experiments of macroamphiphile and payload exchange." Reactive and Functional Polymers 71, no. 3 (March 2011): 303–14. http://dx.doi.org/10.1016/j.reactfunctpolym.2010.10.010.

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Sung Chung, Hoi, Irina V. Gopich, Kevin McHale, John M. Louis, and William A. Eaton. "Measurement of Average Transition-Path Time for Protein Folding in Single Molecule FRET Experiments." Biophysical Journal 102, no. 3 (January 2012): 217a—218a. http://dx.doi.org/10.1016/j.bpj.2011.11.1192.

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Swoboda, Marko, Jörg Henig, Hsin-Mei Cheng, Nicolas Plumere, and Michael Schlierf. "Photostability without pH Drop - An Alternative Oxygen Scavenging System for Sinlge-Molecule FRET Experiments." Biophysical Journal 102, no. 3 (January 2012): 179a. http://dx.doi.org/10.1016/j.bpj.2011.11.972.

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Nagy, Peter, Ágnes Szabó, Tímea Váradi, Tamás Kovács, Gyula Batta, and János Szöllősi. "rFRET: A comprehensive, Matlab-based program for analyzing intensity-based ratiometric microscopic FRET experiments." Cytometry Part A 89, no. 4 (March 22, 2016): 376–84. http://dx.doi.org/10.1002/cyto.a.22828.

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50

Kulesza, Alexander, Steven Daly, Chang Min Choi, Anne-Laure Simon, Fabien Chirot, Luke MacAleese, Rodolphe Antoine, and Philippe Dugourd. "The structure of chromophore-grafted amyloid-β12–28 dimers in the gas-phase: FRET-experiment guided modelling." Physical Chemistry Chemical Physics 18, no. 13 (2016): 9061–69. http://dx.doi.org/10.1039/c6cp00263c.

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Theoretical modelling, ion mobility spectrometry and action-FRET experiments are combined to an experiment guided approach and used to elucidate the structure of chromophore-grafted amyloid-β_12–28 dimers in the gas-phase.

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