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Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.
Hellenkamp, Björn; Schmid, Sonja; Doroshenko, Olga; Opanasyuk, Oleg; Kühnemuth, Ralf; Rezaei Adariani, Soheila; Ambrose, Benjamin; Aznauryan, Mikayel; Barth, Anders; Birkedal, Victoria; Bowen, Mark E; Chen, Hongtao; Cordes, Thorben; Eilert, Tobias; Fijen, Carel; Gebhardt, Christian; Götz, Markus; Gouridis, Giorgos; Gratton, Enrico; Ha, Taekjip; Hao, Pengyu; Hanke, Christian A; Hartmann, Andreas; Hendrix, Jelle; Hildebrandt, Lasse L; Hirschfeld, Verena; Hohlbein, Johannes; Hua, Boyang; Hübner, Christian G; Kallis, Eleni; Kapanidis, Achillefs N; Kim, Jae-Yeol; Krainer, Georg; Lamb, Don C; Lee, Nam Ki; Lemke, Edward A; Levesque, Brié; Levitus, Marcia; McCann, James J; Naredi-Rainer, Nikolaus; Nettels, Daniel; Ngo, Thuy; Qiu, Ruoyi; Robb, Nicole C; Röcker, Carlheinz; Sanabria, Hugo; Schlierf, Michael; Schröder, Tim; Schuler, Benjamin; Seidel, Henning.
Affiliation
  • Hellenkamp B; Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.
  • Schmid S; Engineering and Applied Sciences, Columbia University, New York, NY, USA.
  • Doroshenko O; Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.
  • Opanasyuk O; Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
  • Kühnemuth R; Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
  • Rezaei Adariani S; Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
  • Ambrose B; Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
  • Aznauryan M; Department of Physics and Astronomy, Clemson University, Clemson, SC, USA.
  • Barth A; Department of Chemistry, University of Sheffield, Sheffield, UK.
  • Birkedal V; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark.
  • Bowen ME; Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
  • Chen H; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark.
  • Cordes T; Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA.
  • Eilert T; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
  • Fijen C; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
  • Gebhardt C; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
  • Götz M; Institute for Biophysics, Ulm University, Ulm, Germany.
  • Gouridis G; Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands.
  • Gratton E; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
  • Ha T; Institute of Physical Chemistry, University of Freiburg, Freiburg im Breisgau, Germany.
  • Hao P; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
  • Hanke CA; Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
  • Hartmann A; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
  • Hendrix J; Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA.
  • Hildebrandt LL; Department of Physics, North Carolina State University, Raleigh, NC, USA.
  • Hirschfeld V; Molecular Physical Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
  • Hohlbein J; B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.
  • Hua B; Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Leuven, Belgium.
  • Hübner CG; Dynamic Bioimaging Lab, Advanced Optical Microscopy Center and Biomedical Research Institute, Hasselt University, Hasselt, Belgium.
  • Kallis E; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus, Denmark.
  • Kapanidis AN; Institute of Physics, University of Lübeck, Lübeck, Germany.
  • Kim JY; Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands.
  • Krainer G; Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen, the Netherlands.
  • Lamb DC; Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, USA.
  • Lee NK; Institute of Physics, University of Lübeck, Lübeck, Germany.
  • Lemke EA; Institute for Biophysics, Ulm University, Ulm, Germany.
  • Levesque B; Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.
  • Levitus M; School of Chemistry, Seoul National University, Seoul, South Korea.
  • McCann JJ; B CUBE-Center for Molecular Bioengineering, TU Dresden, Dresden, Germany.
  • Naredi-Rainer N; Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Kaiserslautern, Germany.
  • Nettels D; Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
  • Ngo T; School of Chemistry, Seoul National University, Seoul, South Korea.
  • Qiu R; Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Mainz, Germany.
  • Robb NC; Institute of Molecular Biology (IMB), Mainz, Germany.
  • Röcker C; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
  • Sanabria H; Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA.
  • Schlierf M; School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Schröder T; Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, USA.
  • Schuler B; Physical Chemistry, Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Integrated Protein Science Munich (CiPSM) and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
  • Seidel H; Department of Biochemistry, University of Zurich, Zurich, Switzerland.
Nat Methods ; 15(9): 669-676, 2018 09.
Article in En | MEDLINE | ID: mdl-30171252
ABSTRACT
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Fluorescence Resonance Energy Transfer / Laboratories Type of study: Clinical_trials / Prognostic_studies Language: En Journal: Nat Methods Year: 2018 Document type: Article
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Fluorescence Resonance Energy Transfer / Laboratories Type of study: Clinical_trials / Prognostic_studies Language: En Journal: Nat Methods Year: 2018 Document type: Article