Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Christian Gebhardt, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip HaPengyu Hao, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L. Hildebrandt, Verena Hirschfeld, Johannes Hohlbein, Boyang Hua, Christian G. Hübner, Eleni Kallis, Achillefs N. Kapanidis, Jae Yeol Kim, Georg Krainer, Don C. Lamb, Nam Ki Lee, Edward A. Lemke, Brié Levesque, Marcia Levitus, James J. McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Nicole C. Robb, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Tim Schröder, Benjamin Schuler, Henning Seidel, Lisa Streit, Johann Thurn, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Andrés Manuel Vera, Keith R. Weninger, Bettina Wünsch, Inna S. Yanez-Orozco, Jens Michaelis, Claus A.M. Seidel, Timothy D. Craggs, Thorsten Hugel

Research output: Contribution to journalArticle

40 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)669-676
Number of pages8
JournalNature Methods
Volume15
Issue number9
DOIs
StatePublished - Sep 1 2018

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Benchmarking
Energy Transfer
Energy transfer
Molecules
Structural Models
Biomolecules
Uncertainty
Coloring Agents
DNA
Experiments

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Rezaei Adariani, S., ... Hugel, T. (2018). Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods, 15(9), 669-676. https://doi.org/10.1038/s41592-018-0085-0

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; Streit, Lisa; Thurn, Johann; Tinnefeld, Philip; Tyagi, Swati; Vandenberk, Niels; Vera, Andrés Manuel; Weninger, Keith R.; Wünsch, Bettina; Yanez-Orozco, Inna S.; Michaelis, Jens; Seidel, Claus A.M.; Craggs, Timothy D.; Hugel, Thorsten.

In: Nature Methods, Vol. 15, No. 9, 01.09.2018, p. 669-676.

Research output: Contribution to journalArticle

Hellenkamp, B, Schmid, S, Doroshenko, O, Opanasyuk, O, Kühnemuth, R, Rezaei Adariani, S, Ambrose, B, Aznauryan, M, Barth, A, Birkedal, V, Bowen, ME, Chen, H, Cordes, T, Eilert, T, Fijen, C, Gebhardt, C, Götz, M, Gouridis, G, Gratton, E, Ha, T, Hao, P, Hanke, CA, Hartmann, A, Hendrix, J, Hildebrandt, LL, Hirschfeld, V, Hohlbein, J, Hua, B, Hübner, CG, Kallis, E, Kapanidis, AN, Kim, JY, Krainer, G, Lamb, DC, Lee, NK, Lemke, EA, Levesque, B, Levitus, M, McCann, JJ, Naredi-Rainer, N, Nettels, D, Ngo, T, Qiu, R, Robb, NC, Röcker, C, Sanabria, H, Schlierf, M, Schröder, T, Schuler, B, Seidel, H, Streit, L, Thurn, J, Tinnefeld, P, Tyagi, S, Vandenberk, N, Vera, AM, Weninger, KR, Wünsch, B, Yanez-Orozco, IS, Michaelis, J, Seidel, CAM, Craggs, TD & Hugel, T 2018, 'Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study', Nature Methods, vol. 15, no. 9, pp. 669-676. https://doi.org/10.1038/s41592-018-0085-0
Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S et al. Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. Nature Methods. 2018 Sep 1;15(9):669-676. https://doi.org/10.1038/s41592-018-0085-0
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 ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten. / Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study. In: Nature Methods. 2018 ; Vol. 15, No. 9. pp. 669-676.
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