The DOI matches its Crossref record.
Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The combination of array tomography with FRET enhances the lateral resolution to ~10 nm in the selected single synaptic terminals allowing us to determine whether proteins are close enough to be interacting.
“The combination of array tomography with FRET enhances the lateral resolution to ~ 10 nm in the selected single synaptic terminals allowing us to determine whether proteins are close enough to be interacting [23, 52].”
From Transmembrane protein 97 is a potential synaptic amyloid beta receptor in human Alzheimer’s disease (2024) · cites this paper as [23]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
No references could be resolved yet.
Research works printed but not linked: 51
- Förster, T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann. Phys. 437, 55–75 (1948). · DOI · Paper page
- Stryer, L. & Haugland, R. P. Energy transfer: a spectroscopic ruler. Proc. Natl Acad. Sci. USA 58, 719–726 (1967). · DOI
- Murchie, A. I. et al. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763–766 (1989). · DOI
- Mekler, V. et al. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108, 599–614 (2002). · DOI
- Ha, T. et al. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA 93, 6264–6268 (1996). · DOI
- Schuler, B., Lipman, E. A., Steinbach, P. J., Kumke, M. & Eaton, W. A. Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence. Proc. Natl Acad. Sci. USA 102, 2754–2759 (2005). · DOI
- Choi, U. B. et al. Single-molecule FRET-derived model of the synaptotagmin 1-SNARE fusion complex. Nat. Struct. Mol. Biol. 17, 318–384 (2010). · DOI · Paper page
- Kalinin, S. et al. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nat. Methods 9, 1218–1227 (2012). · DOI
- Hellenkamp, B., Wortmann, P., Kandzia, F., Zacharias, M. & Hugel, T. Multidomain structure and correlated dynamics determined by self-consistent FRET Networks. Nat. Methods 14, 174–180 (2017). · DOI · Paper page
- Eilert, T., Beckers, M., Drechsler, F. & Michaelis, J. Fast-NPS—a Markov chain Monte Carlo-based analysis tool to obtain structural information from single-molecule FRET measurements. Comput. Phys. Commun. 219, 377–389 (2017). · DOI
- Hofmann, D., Korzdorfer, T. & Kummel, S. Energy transfer and Forster’s dipole coupling approximation investigated in a real-time Kohn-Sham scheme. Phys. Rev. A 82, 012509 (2010). · DOI
- Spiegel, J. D., Fulle, S., Kleinschmidt, M., Gohlke, H. & Marian, C. M. Failure of the IDA in FRET systems at close inter-dye distances is moderated by frequent low k 2 values. J. Phys. Chem. B 120, 8845–8862 (2016). · DOI
- Sakon, J. J. & Weninger, K. R. Detecting the conformation of individual proteins in live cells. Nat. Methods 7, 203–205 (2010). · DOI
- Sabanayagam, C. R., Eid, J. S. & Meller, A. Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: corrections due to nonideal transfer. J. Chem. Phys. 122, 61103–61107 (2005). · DOI
- McCann, J. J., Choi, U. B., Zheng, L., Weninger, K. & Bowen, M. E. Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. Biophys. J. 99, 961–970 (2010). · DOI
- Sisamakis, E., Valeri, A., Kalinin, S., Rothwell, P. J. & Seidel, C. A. M. Accurate single-molecule FRET studies using multiparameter fluorescence detection. Methods Enzymol. 475, 455–514 (2010). · DOI
- Lee, N. K. et al. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys. J. 88, 2939–2953 (2005). · DOI
- Kudryavtsev, V. et al. Combining MFD and PIE for accurate single-pair Förster resonance energy transfer measurements. ChemPhysChem 13, 1060–1078 (2012). · DOI
- Hohlbein, J., Craggs, T. D. & Cordes, T. Alternating-laser excitation: single-molecule FRET and beyond. Chem. Soc. Rev. 43, 1156–1171 (2014). · DOI
- Margeat, E. et al. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys. J. 90, 1419–1431 (2006). · DOI
- Muschielok, A. et al. A nano-positioning system for macromolecular structural analysis. Nat. Methods 5, 965–971 (2008). · DOI
- Beckers, M., Drechsler, F., Eilert, T., Nagy, J. & Michaelis, J. Quantitative structural information from single-molecule FRET. Faraday Discuss. 184, 117–129 (2015). · DOI
- Dimura, M. et al. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr. Opin. Struct. Biol. 40, 163–185 (2016). · DOI
- Brunger, A. T., Strop, P., Vrljic, M., Chu, S. & Weninger, K. R. Three-dimensional molecular modeling with single molecule FRET. J. Struct. Biol. 173, 497–505 (2011). · DOI
- Craggs, T. D. et al. Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase. bioRxiv Preprint at https://www.biorxiv.org/content/early/2018/02/10/263038 (2018). · DOI
- Nagy, J., Eilert, T. & Michaelis, J. Precision and accuracy in smFRET based structural studies—a benchmark study of the FAST-Nano-Positioning System. J. Chem. Phys. 148, 123308 (2018). · DOI
- Ivani, I. et al. Parmbsc1: a refined force field for DNA simulations. Nat. Methods 13, 55–58 (2016). · DOI
- Neubauer, H. et al. Orientational and dynamical heterogeneity of rhodamine 6G terminally attached to a DNA helix revealed by NMR and single-molecule fluorescence spectroscopy. J. Am. Chem. Soc. 129, 12746–12755 (2007). · DOI
- Iqbal, A. et al. Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nuclelic acids. Proc. Natl Acad. Sci. USA 105, 11176–11181 (2008). · DOI
- Peulen, T. O., Opanasyuk, O. & Seidel, C. A. M. Combining graphical and analytical methods with molecular simulations to analyze time-resolved FRET-measurements of labeled macromolecules accurately. J. Phys. Chem. B 121, 8211–8241 (2017). · DOI
- Digman, M. A., Caiolfa, V. R., Zamai, M. & Gratton, E. The Phasor approach to fluorescence lifetime imaging analysis. Biophys. J. 84, L14–L16 (2008). · DOI
- Kapanidis, A. N. et al. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc. Natl Acad. Sci. USA 101, 8936–8941 (2004). · DOI
- Müller, B. K., Zaychikov, E., Bräuchle, C. & Lamb, D. C. Pulsed interleaved excitation. Biophys. J. 89, 3508–3522 (2005). · DOI
- Wozniak, A. K., Schröder, G. F., Grubmüller, H., Seidel, C. A. M. & Oesterhelt, F. Single-molecule FRET measures bends and kinks in DNA. Proc. Natl Acad. Sci. USA 105, 18337–18342 (2008). · DOI
- Stelzl, L. S., Erlenbach, N., Heinz, M., Prisner, T. F. & Hummer, G. Resolving the conformational dynamics of DNA with ångström resolution by pulsed electron-electron double resonance and molecular dynamics. J. Am. Chem. Soc. 139, 11674–11677 (2017). · DOI
- Levitus, M. & Ranjit, S. Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Q. Rev. Biophys. 44, 123–151 (2011). · DOI
- Sindbert, S. et al. Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity. J. Am. Chem. Soc. 133, 2463–2480 (2011). · DOI
- Nir, E. et al. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. J. Phys. Chem. B 110, 22103–22124 (2006). · DOI
- Barth, A., Voith von Voithenberg, L. & Lamb, D. C. MFD-PIE and PIE-FI: ways to extract more information with TCSPC. in Advanced Photon Counting Vol. 15 (eds Kapusta, P., Wahl, M. & Erdmann, R.) 129–157 (Springer, Cham, 2015).
- Schmid, S. & Hugel, T. Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties. J. Chem. Phys. 148, 123312 (2018). · DOI
- Preus, S., Hildebrandt, L. L. & Birkedal, V. Optimal background estimators in single-molecule FRET microscopy. Biophys. J. 111, 1278–1286 (2016). · DOI
- Neher, R. & Neher, E. Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. J. Microsc. 213, 46–62 (2004). · DOI
- Hildebrandt, L. L., Preus, S. & Birkedal, V. Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discuss. 184, 131–142 (2015). · DOI
- Deniz, A. A. et al. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Forster distance dependence and subpopulations. Proc. Natl Acad. Sci. USA 96, 3670–3675 (1999). · DOI
- Antonik, M., Felekyan, S., Gaiduk, A. & Seidel, C. A. M. Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. J. Phys. Chem. B 110, 6970–6978 (2006). · DOI
- Kalinin, S., Valeri, A., Antonik, M., Felekyan, S. & Seidel, C. A. M. Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states. J. Phys. Chem. B 114, 7983–7995 (2010). · DOI
- Clegg, R. M. Förster resonance energy transfer—FRET what is it, why do it, and how it’s done. in Laboratory Techniques in Biochemistry and Molecular Biology Vol. 33 (ed Gadella, T. W. J.) 1–57 (Elsevier, Amsterdam, 2009). · DOI
- Braslavsky, S. E. et al. Pitfalls and limitations in the practical use of Förster’s theory of resonance energy transfer. Photochem. Photobiol. Sci. 7, 1444–1448 (2008). · DOI
- Knox, R. S. & van Amerongen, H. Refractive index dependence of the Forster resonance excitation transfer rate. J. Phys. Chem. B 106, 5289–5293 (2002). · DOI
- Voros, J. The density and refractive index of adsorbing protein layers. Biophys. J. 87, 553–561 (2004). · DOI
- Clegg, R. M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353–388 (1992). · DOI
Cited by
Sorted by citations
Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase
Jensen, S. B., Thodberg, S., Parween, S., Moses, M. E., Hansen, C. C., Thomsen, J., Sletfjerding, M. B., Knudsen, C., Del Giudice, R., Lund, P. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22562-w · Cited by 64
Transmembrane protein 97 is a potential synaptic amyloid beta receptor in human Alzheimer’s disease
Colom-Cadena, M., Toombs, J., Simzer, E., Holt, K., McGeachan, R., Tulloch, J., Jackson, R. J., Catterson, J. H., Spires-Jones, M. P., Rose, J., et al. (2024) · Acta Neuropathologica · doi:10.1007/s00401-023-02679-6 · Cited by 44
Metadata
- Authors
- Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kühnemuth, R., Rezaei Adariani, S., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., Bowen, M. E., Chen, H., Cordes, T., Eilert, T., Fijen, C., Gebhardt, C., Götz, M., Gouridis, G., Gratton, E., Ha, T., Hao, P., Hanke, C. A., Hartmann, A., Hendrix, J., Hildebrandt, L. L., Hirschfeld, V., Hohlbein, J., Hua, B., Hübner, C. G., Kallis, E., Kapanidis, A. N., Kim, J.-Y., Krainer, G., Lamb, D. C., Lee, N. K., Lemke, E. A., Levesque, B., Levitus, M., McCann, J. J., Naredi-Rainer, N., Nettels, D., Ngo, T., Qiu, R., Robb, N. C., Röcker, C., Sanabria, H., Schlierf, M., Schröder, T., Schuler, B., Seidel, H., Streit, L., Thurn, J., Tinnefeld, P., Tyagi, S., Vandenberk, N., Vera, A. M., Weninger, K. R., Wünsch, B., Yanez-Orozco, I. S., Michaelis, J., Seidel, C. A. M., Craggs, T. D., & Hugel, T.
- ORCID
- Venue
- Nature Methods
- Published
- 2018-08-31
- Volume
- 15
- Issue
- 9
- Pages
- 669-676
- ISSN
- 1548-7091
- 1548-7105
- PMC
- PMC6121742
- Cited by
- 519
- References
- 0
- Language
- en
- Update notices
- correction (2018-10-16)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review