Monitoring multiple distances within a single molecule using switchable FRET

Uphoff S, Holden SJ, Le Reste L, Periz J, van de Linde S, Heilemann M, Kapanidis AN (2010)
NATURE METHODS 7(10): 831-836.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
The analysis of structure and dynamics of biomolecules is important for understanding their function. Toward this aim, we introduce a method called 'switchable FRET', which combines single-molecule fluorescence resonance energy transfer (FRET) with reversible photoswitching of fluorophores. Typically, single-molecule FRET is measured within a single donor-acceptor pair and reports on only one distance. Although multipair FRET approaches that monitor multiple distances have been developed, they are technically challenging and difficult to extend, mainly because of their reliance on spectrally distinct acceptors. In contrast, switchable FRET sequentially probes FRET between a single donor and spectrally identical photoswitchable acceptors, dramatically reducing the experimental and analytical complexity and enabling direct monitoring of multiple distances. Our experiments on DNA molecules, a protein-DNA complex and dynamic Holliday junctions demonstrate the potential of switchable FRET for studying dynamic, multicomponent biomolecules.
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Zeitschriftentitel
NATURE METHODS
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7
Zeitschriftennummer
10
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831-836
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Uphoff S, Holden SJ, Le Reste L, et al. Monitoring multiple distances within a single molecule using switchable FRET. NATURE METHODS. 2010;7(10):831-836.
Uphoff, S., Holden, S. J., Le Reste, L., Periz, J., van de Linde, S., Heilemann, M., & Kapanidis, A. N. (2010). Monitoring multiple distances within a single molecule using switchable FRET. NATURE METHODS, 7(10), 831-836. doi:10.1038/NMETH.1502
Uphoff, S., Holden, S. J., Le Reste, L., Periz, J., van de Linde, S., Heilemann, M., and Kapanidis, A. N. (2010). Monitoring multiple distances within a single molecule using switchable FRET. NATURE METHODS 7, 831-836.
Uphoff, S., et al., 2010. Monitoring multiple distances within a single molecule using switchable FRET. NATURE METHODS, 7(10), p 831-836.
S. Uphoff, et al., “Monitoring multiple distances within a single molecule using switchable FRET”, NATURE METHODS, vol. 7, 2010, pp. 831-836.
Uphoff, S., Holden, S.J., Le Reste, L., Periz, J., van de Linde, S., Heilemann, M., Kapanidis, A.N.: Monitoring multiple distances within a single molecule using switchable FRET. NATURE METHODS. 7, 831-836 (2010).
Uphoff, Stephan, Holden, Seamus J., Le Reste, Ludovic, Periz, Javier, van de Linde, Sebastian, Heilemann, Mike, and Kapanidis, Achillefs N. “Monitoring multiple distances within a single molecule using switchable FRET”. NATURE METHODS 7.10 (2010): 831-836.

44 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer.
Lerner E, Cordes T, Ingargiola A, Alhadid Y, Chung S, Michalet X, Weiss S., Science 359(6373), 2018
PMID: 29348210
Rediscovering Bacteria through Single-Molecule Imaging in Living Cells.
Kapanidis AN, Lepore A, El Karoui M., Biophys J 115(2), 2018
PMID: 29680157
Ensemble multicolour FRET model enables barcoding at extreme FRET levels.
Dagher M, Kleinman M, Ng A, Juncker D., Nat Nanotechnol 13(10), 2018
PMID: 30061659
The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.
Duchi D, Mazumder A, Malinen AM, Ebright RH, Kapanidis AN., Nucleic Acids Res 46(14), 2018
PMID: 29878276
Investigating supramolecular systems using Förster resonance energy transfer.
Teunissen AJP, Pérez-Medina C, Meijerink A, Mulder WJM., Chem Soc Rev 47(18), 2018
PMID: 30091770
Ultra-Wideband Multi-Dye-Sensitized Upconverting Nanoparticles for Information Security Application.
Lee J, Yoo B, Lee H, Cha GD, Lee HS, Cho Y, Kim SY, Seo H, Lee W, Son D, Kang M, Kim HM, Park YI, Hyeon T, Kim DH., Adv Mater 29(1), 2017
PMID: 27748544
FRET from single to multiplexed signaling events.
Bunt G, Wouters FS., Biophys Rev 9(2), 2017
PMID: 28424742
Single-Molecule Analysis of Bacterial DNA Repair and Mutagenesis.
Uphoff S, Sherratt DJ., Annu Rev Biophys 46(), 2017
PMID: 28375733
Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments.
Jazi AA, Ploetz E, Arizki M, Dhandayuthapani B, Waclawska I, Krämer R, Ziegler C, Cordes T., Biochemistry 56(14), 2017
PMID: 28362086
Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking.
Kawai K, Miyata T, Shimada N, Ito S, Miyasaka H, Maruyama A., Angew Chem Int Ed Engl 56(48), 2017
PMID: 28990725
Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers.
Ploetz E, Lerner E, Husada F, Roelfs M, Chung S, Hohlbein J, Weiss S, Cordes T., Sci Rep 6(), 2016
PMID: 27641327
Single-molecule fluorescence resonance energy transfer in molecular biology.
Sasmal DK, Pulido LE, Kasal S, Huang J., Nanoscale 8(48), 2016
PMID: 27883140
Single-molecule imaging at high fluorophore concentrations by local activation of dye.
Geertsema HJ, Schulte AC, Spenkelink LM, McGrath WJ, Morrone SR, Sohn J, Mangel WF, Robinson A, van Oijen AM., Biophys J 108(4), 2015
PMID: 25692599
How to switch a fluorophore: from undesired blinking to controlled photoswitching.
van de Linde S, Sauer M., Chem Soc Rev 43(4), 2014
PMID: 23942584
Alternating-laser excitation: single-molecule FRET and beyond.
Hohlbein J, Craggs TD, Cordes T., Chem Soc Rev 43(4), 2014
PMID: 24037326
Tracing photon transmission in dye-doped DNA-CTMA optical nanofibers.
Long W, Zou W, Li X, Jiang W, Li X, Chen J., Opt Express 22(6), 2014
PMID: 24663973
Studying the organization of DNA repair by single-cell and single-molecule imaging.
Uphoff S, Kapanidis AN., DNA Repair (Amst) 20(), 2014
PMID: 24629485
Application of fluorescence resonance energy transfer in protein studies.
Ma L, Yang F, Zheng J., J Mol Struct 1077(), 2014
PMID: 25368432
Signal processing for molecular and cellular biological physics: an emerging field.
Little MA, Jones NS., Philos Trans A Math Phys Eng Sci 371(1984), 2013
PMID: 23277603
Helicase-mediated changes in RNA structure at the single-molecule level.
König SL, Liyanage PS, Sigel RK, Rueda D., RNA Biol 10(1), 2013
PMID: 23353571
Non-covalent single transcription factor encapsulation inside a DNA cage.
Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN., Angew Chem Int Ed Engl 52(8), 2013
PMID: 23325751
Real-time observation of multiple-protein complex formation with single-molecule FRET.
Bae W, Choi MG, Hyeon C, Shin YK, Yoon TY., J Am Chem Soc 135(28), 2013
PMID: 23808880
Euler buckling and nonlinear kinking of double-stranded DNA.
Fields AP, Meyer EA, Cohen AE., Nucleic Acids Res 41(21), 2013
PMID: 23956222
Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing.
Krishnan R, Blanco MR, Kahlscheuer ML, Abelson J, Guthrie C, Walter NG., Nat Struct Mol Biol 20(12), 2013
PMID: 24240612
Long-lived intracellular single-molecule fluorescence using electroporated molecules.
Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K, Uphoff S, Kapanidis AN., Biophys J 105(11), 2013
PMID: 24314075
A protein biosensor that relies on bending of single DNA molecules.
Crawford R, Kelly DJ, Kapanidis AN., Chemphyschem 13(4), 2012
PMID: 22368093
DNA-controlled excitonic switches.
Graugnard E, Kellis DL, Bui H, Bui H, Barnes S, Kuang W, Lee J, Hughes WL, Knowlton WB, Yurke B., Nano Lett 12(4), 2012
PMID: 22401838
Advanced fluorescence microscopy techniques--FRAP, FLIP, FLAP, FRET and FLIM.
Ishikawa-Ankerhold HC, Ankerhold R, Drummen GP., Molecules 17(4), 2012
PMID: 22469598
Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET.
Le Reste L, Hohlbein J, Gryte K, Kapanidis AN., Biophys J 102(11), 2012
PMID: 22713582
Advances in quantitative FRET-based methods for studying nucleic acids.
Preus S, Wilhelmsson LM., Chembiochem 13(14), 2012
PMID: 22936620
FRET in cell biology: still shining in the age of super-resolution?
Grecco HE, Verveer PJ., Chemphyschem 12(3), 2011
PMID: 21344589
Improved temporal resolution and linked hidden Markov modeling for switchable single-molecule FRET.
Uphoff S, Gryte K, Evans G, Kapanidis AN., Chemphyschem 12(3), 2011
PMID: 21280168
Single-molecule FRET study of SNARE-mediated membrane fusion.
Diao J, Ishitsuka Y, Bae WR., Biosci Rep 31(6), 2011
PMID: 21919892
Defining the limits of single-molecule FRET resolution in TIRF microscopy.
Holden SJ, Uphoff S, Hohlbein J, Yadin D, Le Reste L, Britton OJ, Kapanidis AN., Biophys J 99(9), 2010
PMID: 21044609
Bright lights, single molecules.
Perkel JM., Biotechniques 49(6), 2010
PMID: 21143208

46 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0
Biology, one molecule at a time.
Kapanidis AN, Strick T., Trends Biochem. Sci. 34(5), 2009
PMID: 19362843
A practical guide to single-molecule FRET.
Roy R, Hohng S, Ha T., Nat. Methods 5(6), 2008
PMID: 18511918

AUTHOR UNKNOWN, 0
Fluorescence resonance energy transfer and nucleic acids.
Clegg RM., Meth. Enzymol. 211(), 1992
PMID: 1406315
Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules.
Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S., Proc. Natl. Acad. Sci. U.S.A. 101(24), 2004
PMID: 15175430
A nano-positioning system for macromolecular structural analysis.
Muschielok A, Andrecka J, Jawhari A, Bruckner F, Cramer P, Michaelis J., Nat. Methods 5(11), 2008
PMID: 18849988
Single-molecule three-color FRET.
Hohng S, Joo C, Ha T., Biophys. J. 87(2), 2004
PMID: 15298935
Three-color single-molecule fluorescence resonance energy transfer.
Clamme JP, Deniz AA., Chemphyschem 6(1), 2005
PMID: 15688649
Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances.
Lee NK, Kapanidis AN, Koh HR, Korlann Y, Ho SO, Kim Y, Gassman N, Kim SK, Weiss S., Biophys. J. 92(1), 2006
PMID: 17040983
Short-range spectroscopic ruler based on a single-molecule optical switch.
Bates M, Blosser TR, Zhuang X., Phys. Rev. Lett. 94(10), 2005
PMID: 15783528
Carbocyanine dyes as efficient reversible single-molecule optical switch.
Heilemann M, Margeat E, Kasper R, Sauer M, Tinnefeld P., J. Am. Chem. Soc. 127(11), 2005
PMID: 15771514
Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM).
Rust MJ, Bates M, Zhuang X., Nat. Methods 3(10), 2006
PMID: 16896339
Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes.
Heilemann M, van de Linde S, Schuttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M., Angew. Chem. Int. Ed. Engl. 47(33), 2008
PMID: 18646237
Optical lock-in detection of FRET using synthetic and genetically encoded optical switches.
Mao S, Benninger RK, Yan Y, Petchprayoon C, Jackson D, Easley CJ, Piston DW, Marriott G., Biophys. J. 94(11), 2008
PMID: 18281383
FRET imaging.
Jares-Erijman EA, Jovin TM., Nat. Biotechnol. 21(11), 2003
PMID: 14595367
Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy.
Vogelsang J, Cordes T, Forthmann C, Steinhauer C, Tinnefeld P., Proc. Natl. Acad. Sci. U.S.A. 106(20), 2009
PMID: 19433792
Super-resolution imaging with small organic fluorophores.
Heilemann M, van de Linde S, Mukherjee A, Sauer M., Angew. Chem. Int. Ed. Engl. 48(37), 2009
PMID: 19670280
Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation.
Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S., Biophys. J. 88(4), 2005
PMID: 15653725
Single-molecule FRET measures bends and kinks in DNA.
Wozniak AK, Schroder GF, Grubmuller H, Seidel CA, Oesterhelt F., Proc. Natl. Acad. Sci. U.S.A. 105(47), 2008
PMID: 19020079
Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes.
Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S., Biophys. J. 90(4), 2005
PMID: 16299085
Nonblinking and long-lasting single-molecule fluorescence imaging.
Rasnik I, McKinney SA, Ha T., Nat. Methods 3(11), 2006
PMID: 17013382
Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH., Cell 108(5), 2002
PMID: 11893332
Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer.
Clegg RM, Murchie AI, Zechel A, Lilley DM., Proc. Natl. Acad. Sci. U.S.A. 90(7), 1993
PMID: 8464916

AUTHOR UNKNOWN, 0
Catabolite activator protein: DNA binding and transcription activation.
Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH., Curr. Opin. Struct. Biol. 14(1), 2004
PMID: 15102444
Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.
Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH., J. Mol. Biol. 312(3), 2001
PMID: 11563909
Holliday junction dynamics and branch migration: single-molecule analysis.
Karymov M, Daniel D, Sankey OF, Lyubchenko YL., Proc. Natl. Acad. Sci. U.S.A. 102(23), 2005
PMID: 15917329
Analysis of single-molecule FRET trajectories using hidden Markov modeling.
McKinney SA, Joo C, Ha T., Biophys. J. 91(5), 2006
PMID: 16766620
Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley ND, Kapanidis AN., Proc. Natl. Acad. Sci. U.S.A. 107(2), 2009
PMID: 20080740
Single-molecule FRET analysis of protein-DNA complexes.
Heilemann M, Hwang LC, Lymperopoulos K, Kapanidis AN., Methods Mol. Biol. 543(), 2009
PMID: 19378183

AUTHOR UNKNOWN, 0
On the mechanism of Trolox as antiblinking and antibleaching reagent.
Cordes T, Vogelsang J, Tinnefeld P., J. Am. Chem. Soc. 131(14), 2009
PMID: 19301868

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Forster distance dependence and subpopulations.
Deniz AA, Dahan M, Grunwell JR, Ha T, Faulhaber AE, Chemla DS, Weiss S, Schultz PG., Proc. Natl. Acad. Sci. U.S.A. 96(7), 1999
PMID: 10097095
Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies.
Norman DG, Grainger RJ, Uhrin D, Lilley DM., Biochemistry 39(21), 2000
PMID: 10828944
Cy3B: improving the performance of cyanine dyes.
Cooper M, Ebner A, Briggs M, Burrows M, Gardner N, Richardson R, West R., J Fluoresc 14(2), 2004
PMID: 15615040

AUTHOR UNKNOWN, 0
FRET or no FRET: a quantitative comparison.
Berney C, Danuser G., Biophys. J. 84(6), 2003
PMID: 12770904

Daigle, Proc. SPIE. 6276(), 2006
Precise nanometer localization analysis for individual fluorescent probes.
Thompson RE, Larson DR, Webb WW., Biophys. J. 82(5), 2002
PMID: 11964263
Structural dynamics of individual Holliday junctions.
McKinney SA, Declais AC, Lilley DM, Ha T., Nat. Struct. Biol. 10(2), 2003
PMID: 12496933

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