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Imaging biological structures with fluorescence photoactivation localization microscopy
Open accessAbstract
Fluorescence photoactivation localization microscopy (FPALM) images biological structures with subdiffraction-limited resolution. With repeated cycles of activation, readout and bleaching, large numbers of photoactivatable probes can be precisely localized to obtain a map (image) of labeled molecules with an effective resolution of tens of nanometers. FPALM has been applied to a variety of biological imaging applications, including membrane, cytoskeletal and cytosolic proteins in fixed and living cells. Molecular motions can be quantified. FPALM can also be applied to nonbiological samples, which can be labeled with photoactivatable probes. With emphasis on cellular imaging, we describe here the adaptation of a conventional widefield fluorescence microscope for FPALM and present step-by-step procedures to successfully obtain and analyze FPALM images. The fundamentals of this protocol may also be applicable to users of similar imaging techniques that apply localization of photoactivatable probes to achieve super-resolution. Once alignment of the setup has been completed, data acquisitions can be obtained in approximately 1–30 min and analyzed in approximately 0.5–4 h.
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Hell, S. W. (2007) · Science · doi:10.1126/science.1137395 · Cited by 2,967
Precise Nanometer Localization Analysis for Individual Fluorescent Probes
Thompson, R. E., Larson, D. R., & Webb, W. W. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75618-x · Cited by 2,320
Research works printed but not linked: 54
- Born, M. & Wolf, E. Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Cambridge University Press, New York, 1997).
- Hell, S.W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780–782 (1994). · DOI · Paper page
- Hess, S.T., Girirajan, T.P. & Mason, M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy (FPALM). Biophys. J. 91, 4258–4272 (2006). · DOI · Paper page
- Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006). · DOI · Paper page
- Rust, M.J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–796 (2006). · DOI · Paper page
- Hess, S.T. et al. Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories. Proc. Natl. Acad. Sci. USA 104, 17370–17375 (2007). · DOI · Paper page
- Geisler, C. et al. Resolution of λ/10 in fluorescence microscopy using fast single molecule photo-switching. Appl. Phys. A 88, 223–226 (2007). · DOI
- Flors, C. et al. A stroboscopic approach for fast photoactivation-localization microscopy with dronpa mutants. J. Am. Chem. Soc. 129, 13970–13977 (2007). · DOI
- Manley, S. et al. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat. Methods 5, 155–157 (2008). · DOI · Paper page
- Shroff, H., Galbraith, C.G., Galbraith, J.A. & Betzig, E. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat. Methods 5, 417–423 (2008). · DOI · Paper page
- Bates, M., Huang, B., Dempsey, G.T. & Zhuang, X. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317, 1749–1753 (2007). · DOI · Paper page
- Shroff, H. et al. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc. Natl. Acad. Sci. USA 104, 20308–20313 (2007). · DOI · Paper page
- Bock, H. et al. Two-color far-field fluorescence nanoscopy based on photo-switchable emitters. Appl. Phys. B 88, 161–165 (2007). · DOI · Paper page
- Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008). · DOI · Paper page
- Juette, M.F. et al. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat. Methods 5, 527–529 (2008). · DOI · Paper page
- Huang, B., Jones, S.A., Brandenburg, B. & Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5, 1047–1052 (2008). · DOI · Paper page
- Gould, T.J. et al. Nanoscale imaging of molecular positions and anisotropies. Nat. Methods 5, 1027–1030 (2008). · DOI
- Bates, M., Blosser, T.R. & Zhuang, X. Short-range spectroscopic ruler based on a single-molecule optical switch. Phys. Rev. Lett. 94, 108101 (2005). · DOI · Paper page
- Lukyanov, K.A., Chudakov, D.M., Lukyanov, S. & Verkhusha, V.V. Innovation: photoactivatable fluorescent proteins. Nat. Rev. Mol. Cell Biol. 6, 885–891 (2005). · DOI · Paper page
- Patterson, G.H. & Lippincott-Schwartz, J. A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297, 1873–1877 (2002). · DOI · Paper page
- Chudakov, D.M. et al. Photoswitchable cyan fluorescent protein for protein tracking. Nat. Biotechnol. 22, 1435–1439 (2004). · DOI · Paper page
- Verkhusha, V.V. & Sorkin, A. Conversion of the monomeric red fluorescent protein into a photoactivatable probe. Chem. Biol. 12, 279–85 (2005). · DOI
- Subach, F.V. et al. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat. Methods (in press).
- van Thor, J.J., Gensch, T., Hellingwerf, K.J. & Johnson, L.N. Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222. Nat. Struct. Biol. 9, 37–41 (2002). · doi:10.1038/nsb739
- Tsien, R.Y. The green fluorescent protein. Annu. Rev. Biochem. 67, 509–544 (1998). · DOI · Paper page
- Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H. & Miyawaki, A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl. Acad. Sci. USA 99, 12651–12656 (2002). · DOI · Paper page
- Wiedenmann, J. et al. EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion. Proc. Natl. Acad. Sci. USA 101, 15905–15910 (2004). · DOI · Paper page
- Tsutsui, H., Karasawa, S., Shimizu, H., Nukina, N. & Miyawaki, A. Semi-rational engineering of a coral fluorescent protein into an efficient highlighter. EMBO Rep. 6, 233–238 (2005). · DOI · Paper page
- Gurskaya, N.G. et al. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat. Biotechnol. 24, 461–465 (2006). · DOI · Paper page
- Chudakov, D.M., Lukyanov, S. & Lukyanov, K.A. Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and dendra2. Nat. Protoc. 2, 2024–2032 (2007). · DOI · Paper page
- Chudakov, D.M. et al. Kindling fluorescent proteins for precise in vivo photolabeling. Nat. Biotechnol. 21, 191–194 (2003). · DOI · Paper page
- Ando, R., Mizuno, H. & Miyawaki, A. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306, 1370–1373 (2004). · DOI · Paper page
- Stiel, A.C. et al. 1.8 a bright-state structure of the reversibly switchable fluorescent protein dronpa guides the generation of fast switching variants. Biochem. J. 402, 35–42 (2007). · DOI · Paper page
- Ando, R., Flors, C., Mizuno, H., Hofkens, J. & Miyawaki, A. Highlighted generation of fluorescence signals using simultaneous two-color irradiation on dronpa mutants. Biophys. J. 92, L97–L99 (2007). · DOI
- Zacharias, D.A., Violin, J.D., Newton, A.C. & Tsien, R.Y. Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296, 913–916 (2002). · DOI · Paper page
- Egner, A. et al. Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys. J. 93, 3285–3290 (2007). · DOI · Paper page
- Haupts, U., Maiti, S., Schwille, P. & Webb, W.W. Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy. Proc. Natl. Acad. Sci. USA 95, 13573–13578 (1998). · DOI · Paper page
- Schwille, P., Kummer, S., Heikal, A.A., Moerner, W.E. & Webb, W.W. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA 97, 151–156 (2000). · DOI · Paper page
- Heikal, A.A., Hess, S.T., Baird, G.S., Tsien, R.Y. & Webb, W.W. Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: Coral red (dsred) and yellow (citrine). Proc. Natl. Acad. Sci. USA 97, 11996–12001 (2000). · DOI · Paper page
- Dickson, R.M., Cubitt, A.B., Tsien, R.Y. & Moerner, W.E. On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature 388, 355–358 (1997). · DOI · Paper page
- Enderlein, J., Toprak, E. & Selvin, P.R. Polarization effect on position accuracy of fluorophore localization. Opt. Expr. 14, 8111–8120 (2006). · DOI · Paper page
- Shaner, N.C., Patterson, G.H. & Davidson, M.W. Advances in fluorescent protein technology. J. Cell Sci. 120, 4247–4260 (2007). · DOI · Paper page
- Ha, T. Single-molecule fluorescence resonance energy transfer. Methods 25, 78–86 (2001). · DOI · Paper page
- Hess, S.T., Gould, T.J., Gunewardene, M., Bewersdorf, J. & Mason, M.D. Ultra-high resolution imaging of biomolecules by fluorescence photoactivation localization microscopy (FPALM). In Methods in Molecular Biology (eds. Foote, R.S. & Lee, J.W.) in press (Humana Press, Totowa, NJ).
- Self, S.A. Focusing of spherical Gaussian beams. Appl. Opt. 22, 658 (1983). · doi:10.1364/ao.22.000658
- Currie, L.A. Limits for qualitative detection and quantitative determination. Anal. Chem. 40, 586–593 (1968). · DOI · Paper page
- Gordon, M.P., Ha, T. & Selvin, P.R. Single-molecule high-resolution imaging with photobleaching. Proc. Natl. Acad. Sci. USA 101, 6462–6465 (2004). · DOI · Paper page
- Qu, X., Wu, D., Mets, L. & Scherer, N.F. Nanometer-localized multiple single-molecule fluorescence microscopy. Proc. Natl. Acad. Sci. USA 101, 11298–11303 (2004). · DOI · Paper page
- Cheezum, M.K., Walker, W.F. & Guilford, W.H. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J. 81, 2378–2388 (2001). · DOI · Paper page
- Pawley, J.B. Handbook of Biological Confocal Microscopy (Plenum Press, New York, 1995). · DOI · Paper page
- Ripley, B.D. Tests of randomness for spatial point patterns. J. R. Stat. Soc. Ser. B 41, 368–374 (1979). · DOI · Paper page
- Pathria, R.K. Statistical Mechanics (Butterworth-Heinemann, Oxford, Boston, 1996).
- Lakowicz, J.R. Principles of Fluorescence Spectroscopy (Springer Science, New York, 2006). · DOI · Paper page
- Sternberg, S.R. Biomedical image processing. IEEE Comput. 16, 22–34 (1983). · DOI · Paper page
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Metadata
- Authors
- Gould, T. J., Verkhusha, V. V., & Hess, S. T.
- Venue
- Nature Protocols
- Published
- 2009-02-12
- Volume
- 4
- Issue
- 3
- Pages
- 291-308
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W1997107435
- Cited by
- 194
- References
- 2
- FWCI
- 9.75
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.springer.com/tdm (tdm)
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