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Ultrahigh Resolution Imaging of Biomolecules by Fluorescence Photoactivation Localization Microscopy

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Book cover Micro and Nano Technologies in Bioanalysis

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 544))

Summary

Diffraction limits the biological structures that can be imaged by normal light microscopy. However, recently developed techniques are breaking the limits that diffraction poses and allowing imaging of biological samples at the molecular length scale. Fluorescence photoactivation localization microscopy (FPALM) and related methods can now image molecular distributions in fixed and living cells with measured resolution better than 30 nm. Based on localization of single photoactivatable molecules, FPALM uses repeated cycles of activation, localization, and photobleaching, combined with high-sensitivity fluorescence imaging, to identify and localize large numbers of molecules within a sample. Procedures and pitfalls for construction and use of such a microscope are discussed in detail. Representative images of cytosolic proteins, membrane proteins, and other structures, as well as examples of results during acquisition are shown. It is hoped that these details can be used to perform FPALM on a variety of biological samples, to significantly advance the understanding of biological systems.

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References

  1. Pawley, J. B. (2006). Handbook of Biological Confocal Microscopy, 3rd ed., Springer, New York, NY.

    Book  Google Scholar 

  2. Abbe, E. (1873). Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung, Archive für mikroskopische Anatomie 9, 413–68.

    Article  Google Scholar 

  3. Sandison, D. R., Piston, D. W., Williams, R. M.and Webb, W. W. (1995). Quantitative comparison of background rejection, signal-to-noise ratio, and resolution in confocal and full-field laser-scanning microscopes, Appl Opt 34, 3576–88.

    Article  CAS  Google Scholar 

  4. Gu, M. (1999). Advanced Optical Imaging Theory, Springer, Heidelberg.

    Google Scholar 

  5. Sandison, D. R. and Webb, W. W. (1994). Background rejection and signal-to-noise optimization in confocal and alternative fluorescence microscopes, Appl Opt 33, 603–15.

    Article  CAS  Google Scholar 

  6. Yildiz, A., Forkey, J. N., McKinney, S. A., Ha, T., Goldman, Y. E. and Selvin, P. R. (2003). Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization, Science 300, 2061–5.

    Article  CAS  Google Scholar 

  7. Barak, L. S. and Webb, W. W. (1982). Diffusion of low density lipoprotein-receptor complex on human fibroblasts, J Cell Biol 95, 846–52.

    Article  CAS  Google Scholar 

  8. Lakowicz, J. R. (2006). Principles of Fluorescence Spectroscopy, 3rd ed., Springer, New York.

    Book  Google Scholar 

  9. Gustafsson, M. G. (2000). Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy., J Microsc 198, 82–7.

    Article  CAS  Google Scholar 

  10. Hell, S. and Steltzer, E. H. K. (1992). Properties of a 4Pi confocal fluorescence microscope, J Opt Soc Am A 9, 2159–67.

    Article  Google Scholar 

  11. Bewersdorf, J., Bennett, B. T. and Knight, K. L. (2006). H2AX chromatin structures and their response to DNA damage revealed by 4Pi microscopy, Proc Natl Acad Sci U S A 103, 18137–42.

    Article  CAS  Google Scholar 

  12. Egner, A., Jakobs, S. and Hell, S. W. (2002). Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast, Proc Natl Acad Sci U S A 99, 3370–5.

    Article  CAS  Google Scholar 

  13. Gugel, H., Bewersdorf, J., Jakobs, S., Engelhardt, J., Storz, R. and Hell, S. W. (2004). Cooperative 4Pi excitation and detection yields sevenfold sharper optical sections in live-cell microscopy, Biophys J 87, 4146–52.

    Article  CAS  Google Scholar 

  14. Bewersdorf, J., Schmidt, R. and Hell, S. W. (2006). Comparison of I5M and 4Pi-microscopy, J Microsc 222, 105–17.

    Article  CAS  Google Scholar 

  15. Gustafsson, M. G., Agard, D. A. and Sedat, J. W.(1995). Sevenfold improvement of axial resolution in 3D widefield microscopy using two objective lenses, Proc SPIE 2412, 147–56.

    Article  Google Scholar 

  16. Gustafsson, M. G., Agard, D. A. and Sedat, J. W. (1999). I5M: 3D widefield light microscopy with better than 100 nm axial resolution, J Microsc 195, 10–6.

    Article  CAS  Google Scholar 

  17. Hell, S. W. and Wichmann, J. (1994). Breaking the diffraction resolution limit by stimulated-emission – stimulated-emission-depletion fluorescence microscopy, Opt Lett 19, 780–82.

    Article  CAS  Google Scholar 

  18. Westphal, V. and Hell, S. W. (2005). Nanoscale resolution in the focal plane of an optical microscope, Phys Rev Lett 94, 143903.

    Article  Google Scholar 

  19. Kittel, R. J., Wichmann, C., Rasse, T. M., Fouquet, W., Schmidt, M., Schmid, A., Wagh, D. A., Pawlu, C., Kellner, R. R., Willig, K. I., Hell, S. W., Buchner, E., Heckmann, M. and Sigrist, S. J. (2006). Bruchpilot promotes active zone assembly, Ca2+ channel clustering, and vesicle release, Science 312, 1051–4.

    Article  CAS  Google Scholar 

  20. Terskikh, A., Fradkov, A., Ermakova, G., Zaraisky, A., Tan, P., Kajava, A. V., Zhao, X. N., Lukyanov, S., Matz, M., Kim, S., Weissman, I. and Siebert, P. (2000). “Fluorescent timer”: protein that changes color with time, Science 290, 1585–88.

    Article  CAS  Google Scholar 

  21. Hell, S. W. and Kroug, M. (1995). Ground-state depletion fluorescence microscopy, a concept for breaking the diffraction resolution limit, Appl Phys B 60, 495–97.

    Article  Google Scholar 

  22. Lidke, K. A., Rieger, B., Jovin, T. M. and Heintzmann, R. (2005). Superresolution by localization of quantum dots using blinking statistics, Opt Express 13, 7052–62.

    Article  Google Scholar 

  23. Gustafsson, M. G. (2005). Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution, Proc Natl Acad Sci U S A 102, 13081–6.

    Article  CAS  Google Scholar 

  24. Hofmann, M., Eggeling, C., Jakobs, S. and Hell, S. W. (2005). Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins, Proc Natl Acad Sci U S A 102, 17565–9.

    Article  CAS  Google Scholar 

  25. Burns, D. H., Callis, J. B., Christian, G. D. and Davidson, E. R. (1985). Strategies for attaining superresolution using spectroscopic data as constraints, Appl Opt 24, 154.

    Article  CAS  Google Scholar 

  26. Hwang, J., Tamm, L. K., Bohm, C., Ramalingam, T. S., Betzig, E. and Edidin, M. (1995). Nanoscale complexity of phospholipid monolayers investigated by near-field scanning optical microscopy, Science 270, 610–14.

    Article  CAS  Google Scholar 

  27. Esa, A., Edelmann, P., Kreth, G., Trakhtenbrot, L., Amariglio, N., Rechavi, G., Hausmann, M. and Cremer, C. (2000). Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome, J Microsc 199, 96–105.

    Article  CAS  Google Scholar 

  28. Kural, C., Kim, H., Syed, S., Goshima, G., Gelfand, V. I. and Selvin, P. R. (2005). Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement?, Science 308, 1469–72.

    Article  CAS  Google Scholar 

  29. Qu, X., Wu, D., Mets, L. and Scherer, N. F. (2004). Nanometer-localized multiple single-molecule fluorescence microscopy, Proc Natl Acad Sci U S A 101, 11298–303.

    Article  CAS  Google Scholar 

  30. Gordon, M. P., Ha, T. and Selvin, P. R. (2004). Single-molecule high-resolution imaging with photobleaching, Proc Natl Acad Sci U S A 101, 6462–5.

    Article  CAS  Google Scholar 

  31. Bates, M., Huang, B., Dempsey, G. T. and Zhuang, X. (2007). Multicolor super-resolution imaging with photo-switchable fluorescent probes, Science 317, 1749–53.

    Article  CAS  Google Scholar 

  32. Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., Davidson, M. W., Lippincott-Schwartz, J. and Hess, H. F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution, Science 313, 1642–45.

    Article  CAS  Google Scholar 

  33. Rust, M. J., Bates, M. and Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nat Methods 3, 793–6.

    Article  CAS  Google Scholar 

  34. Egner, A., Geisler, C., von Middendorff, C., Bock, H., Wenzel, D., Medda, R., Andresen, M., Stiel, A. C., Jakobs, S., Eggeling, C., Schonle, A. and Hell, S. W. (2007). Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters, Biophys J 93, 3285–90.

    Article  CAS  Google Scholar 

  35. Folling, J., Belov, V., Kunetsky, R., Medda, R., Schonle, A., Egner, A., Eggeling, C., Bossi, M. and Hell, S. W. (2007). Photochromic rhodamines provide nanoscopy with optical sectioning, Angew Chem Int Ed Engl 46, 6266–70.

    Article  CAS  Google Scholar 

  36. Thompson, R. E., Larson, D. R. and Webb, W. W. (2002). Precise nanometer localization analysis for individual fluorescent probes, Biophys J 82, 2775–83.

    Article  CAS  Google Scholar 

  37. Lacoste, T. D., Michalet, X., Pinaud, F., Chemla, D. S., Alivisatos, A. P. and Weiss, S. (2000). Ultrahigh-resolution multicolor colocalization of single fluorescent probes, Proc Natl Acad Sci U S A 97, 9461–6.

    Article  CAS  Google Scholar 

  38. Michalet, X. and Weiss, S. (2006). Using photon statistics to boost microscopy resolution, Proc Natl Acad Sci U S A 103, 4797–98.

    Article  CAS  Google Scholar 

  39. Lukyanov, K. A., Chudakov, D. M., Lukyanov, S. and Verkhusha, V. V. (2005). Photoactivatable fluorescent proteins, Nat Rev Mol Cell Biol 6, 885–91.

    Article  CAS  Google Scholar 

  40. Tsien, R. Y. (1998). The green fluorescent protein, Annu Rev Biochem 67, 509–44.

    Article  CAS  Google Scholar 

  41. Giepmans, B. N., Adams, S. R., Ellisman, M. H. and Tsien, R. Y. (2006). The fluorescent toolbox for assessing protein location and function, Science 312, 217–24.

    Article  CAS  Google Scholar 

  42. Hess, S. T., Girirajan, T. P. and Mason, M. D. (2006). Ultra-high resolution imaging by fluorescence photoactivation localization microscopy, Biophys J 91, 4258–72.

    Article  CAS  Google Scholar 

  43. Hess, S. T., Sheets, E. D., Wagenknecht-Wiesner, A. and Heikal, A. A. (2003). Quantitative Analysis of the fluorescence properties of intrinsically fluorescent proteins in living cells, Biophys J 85, 2566–80.

    Article  CAS  Google Scholar 

  44. Heikal, A. A., Hess, S. T. and Webb, W. W. (2001). Multiphoton molecular spectroscopy and excited–state dynamics of enhanced green fluorescent protein (EGFP): acid-base specificity, Chem Phys 274, 37–55.

    Article  CAS  Google Scholar 

  45. Haupts, U., Maiti, S., Schwille, P. and Webb, W. W. (1998). Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy, Proc Natl Acad Sci U S A 95, 13573–78.

    Article  CAS  Google Scholar 

  46. Hess, S. T., Heikal, A. A. and Webb, W. W. (2004). Fluorescence photoconversion kinetics in novel green fluorescent protein pH sensors, J Phys Chem B 108, 10138–48.

    Article  CAS  Google Scholar 

  47. Heikal, A. A., Hess, S. T., Baird, G. S., Tsien, R. Y. and Webb, W. W. (2000). Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: Coral red (dsRed) and yellow (Citrine), Proc Natl Acad Sci U S A 97, 11996–2001.

    Article  CAS  Google Scholar 

  48. Schwille, P., Kummer, S., Heikal, A. A., Moerner, W. E. and Webb, W. W. (2000). Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins, Proc Natl Acad Sci U S A 97, 151–56.

    Article  CAS  Google Scholar 

  49. Brasselet, S., Peterman, E. J. G., Miyawaki, A. and Moerner, W. E. (2000). Single-molecule fluorescence resonant energy transfer in calcium concentration dependent cameleon, J Phys Chem B 104, 3676–82.

    Article  CAS  Google Scholar 

  50. Patterson, G. H. and Lippincott-Schwartz, J. (2002). A photoactivatable GFP for selective photolabeling of proteins and cells, Science 297, 1873–77.

    Article  CAS  Google Scholar 

  51. Chudakov, D. M., Verkhusha, V. V., Staroverov, D. B., Souslova, E. A., Lukyanov, S. and Lukyanov, K. A. (2004). Photoswitchable cyan fluorescent protein for protein tracking, Nat Biotechnol 22, 1435–9.

    Article  CAS  Google Scholar 

  52. Wiedenmann, J., Ivanchenko, S., Oswald, F., Schmitt, F., Rocker, C., Salih, A., Spindler, K. D. and Nienhaus, G. U. (2004). EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion, Proc Natl Acad Sci U S A 101, 15905–10.

    Article  CAS  Google Scholar 

  53. Gurskaya, N. G., Verkhusha, V. V., Shcheglov, A. S., Staroverov, D. B., Chepurnykh, T. V., Fradkov, A. F., Lukyanov, S. and Lukyanov, K. A. (2006). Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light, Nat Biotechnol 24, 461–65.

    Article  CAS  Google Scholar 

  54. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H. and Miyawaki, A. (2002). An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein, Proc Natl Acad Sci U S A 99, 12651–56.

    Article  CAS  Google Scholar 

  55. Ando, R., Mizuno, H. and Miyawaki, A. (2004). Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting, Science 306, 1370–73.

    Article  CAS  Google Scholar 

  56. Axelrod, D. (2001) Total internal reflection fluorescence microscopy in cell biology, Traffic 2, 764–74.

    Article  CAS  Google Scholar 

  57. Axelrod, D., Thompson, N. L. and Burghardt, T. P. (1983). Total internal inflection fluorescent microscopy, J Microsc 129, 19–28.

    Article  CAS  Google Scholar 

  58. Hess, S. T., Gould, T. J., Gudheti, M. V., Maas, S. A., Mills, K. D. and Zimmerberg, J. (2007). Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories, Proc Natl Acad Sci U S A 104, 17370–75.

    Article  CAS  Google Scholar 

  59. Lakowicz, J. R. (1983). Principles of Fluorescence Spectroscopy, Plenum, New York.

    Book  Google Scholar 

  60. Bass, M. and Optical Society of America. (1995).Handbook of Optics, 2nd ed., McGraw-Hill, New York.

    Google Scholar 

  61. Sternberg, S. R. (1983). Biomedical image processing, IEEE Comput 22–34.

    Google Scholar 

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Acknowledgments

The authors thank J. Zimmerberg and P. Blank for useful discussions and loaned equipment, G. Patterson for PA-GFP protein and constructs, J. Wiedenmann and U. Nienhaus for EosFP protein and constructs, J. Gosse for helpful discussions, V. Verkhusha for Dendra2 constructs, T. Tripp for machining services, and J. Lozier for molecular biology services. This work was supported in part by National Institutes of Health (NIH) grant K25-AI65459, National Science Foundation (NSF) grant CHE-0722759, and University of Maine startup funds.

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Hess, S.T., Gould, T.J., Gunewardene, M., Bewersdorf, J., Mason, M.D. (2009). Ultrahigh Resolution Imaging of Biomolecules by Fluorescence Photoactivation Localization Microscopy. In: Foote, R., Lee, J. (eds) Micro and Nano Technologies in Bioanalysis. Methods in Molecular Biology™, vol 544. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-483-4_32

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  • DOI: https://doi.org/10.1007/978-1-59745-483-4_32

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