Fluorescence Labeling

Fluorescence Microscopy: From Principles to Biological Applications

Volumn , Issue , 2013, Pages 143-173

  Nienhaus, Gerd Ulrich ^a,b   Nienhaus, Karin ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

Green fluorescent protein; Labeling technique; Live cell dynamics; Nanoparticle; Photoactivatable fluorescent protein

Indexed keywords

EID: 84884639784     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527671595.ch4     Document Type: Chapter

References (94)

1. Adam, V., Lelimousin, M., Boehme, S., Desfonds, G., Nienhaus, K., Field, M.J., Wiedenmann, J., McSweeney, S., Nienhaus, G.U., and Bourgeois, D. (2008) Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations. Proc. Natl. Acad. Sci. U.S.A., 105, 18343-18348.
2. Adams, S.R., Campbell, R.E., Gross, L.A., Martin, B.R., Walkup, G.K., Yao, Y., Llopis, J., and Tsien, R.Y. (2002) New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc., 124, 6063-6076.
3. Aitken, C.E., Marshall, R.A., and Puglisi, J.D. (2008) An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys. J., 94, 1826-1835.
4. 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, 12651-12656.
5. Baker, S.N. and Baker, G.A. (2010) Luminescent carbon nanodots: emergent nanolights. Angew. Chem. Int. Ed., 49, 6726-6744.
6. Barondeau, D.P., Kassmann, C.J., Tainer, J.A., and Getzoff, E.D. (2002) Structural chemistry of a green fluorescent protein Zn biosensor. J. Am. Chem. Soc., 124, 3522-3524.
7. Biju, V., Itoh, T., and Ishikawa, M. (2010) Delivering quantum dots to cells: bioconjugated quantum dots for targeted and nonspecific extracellular and intracellular imaging. Chem. Soc. Rev., 39, 3031-3056.
8. Breus, V.V., Heyes, C.D., Tron, K., and Nienhaus, G.U. (2009) Zwitterionic biocompatible quantum dots for wide pH stability and weak nonspecific binding to cells. ACS Nano, 3, 2573-2580.
9. Chen, I., Howarth, M., Lin, W., and Ting, A.Y. (2005) Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nat. Methods, 2, 99-104.
10. Chin, J.W., Cropp, T.A., Anderson, J.C., Mukherji, M., Zhang, Z., and Schultz, P.G. (2003) An expanded eukaryotic genetic code. Science, 301, 964-967.
11. Chudakov, D.M., Belousov, V.V., Zaraisky, A.G., Novoselov, V.V., Staroverov, D.B., Zorov, D.B., Lukyanov, S., and Lukyanov, K.A. (2003) Kindling fluorescent proteins for precise in vivo photolabeling. Nat. Biotechnol., 21, 191-194.
12. Cordes, T., Vogelsang, J., and Tinnefeld, P. (2009) On the mechanism of Trolox as antiblinking and antibleaching reagent. J. Am. Chem. Soc., 131, 5018-5019.
13. Daniel, M.C. and Astruc, D. (2004) Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem. Rev., 104, 293-346.
14. Day, R.N. and Schaufele, F. (2008) Fluorescent protein tools for studying protein dynamics in living cells: a review. J. Biomed. Opt., 13, 031202.
15. Duan, H. and Nie, S. (2007) Etching colloidal gold nanocrystals with hyperbranched and multivalent polymers: a new route to fluorescent and water-soluble atomic clusters. J. Am. Chem. Soc., 129, 2412-2413.
16. Ebbinghaus, S., Dhar, A., McDonald, J.D., and Gruebele, M. (2010) Protein folding stability and dynamics imaged in a living cell. Nat. Methods, 7, 319-323.
17. Elsliger, M.A., Wachter, R.M., Hanson, G.T., Kallio, K., and Remington, S.J. (1999a) Structural and spectral response of green fluorescent protein variants to changes in pH. Biochemistry, 38, 5296-5301.
18. Elsliger, M.A., Wachter, R.M., Hanson, G.T., Kallio, K., and Remington, S.J. (1999b) Structural and spectral response of green fluorescent protein variants to changes in pH. Biochemistry, 38, 5296-5301.
19. Fan, J. and Chu, P.K. (2010) Group iv nanoparticles: synthesis, properties, and biological applications. Small, 6, 2080-2098.
20. Fuchs, J., Böhme, S., Oswald, F., Hedde, P.N., Krause, M., Wiedenmann, J., and Nienhaus, G.U. (2010) A photoactivatable marker protein for pulse-chase imaging with superresolution. Nat. Methods, 7, 627-630.
21. Gautier, A., Juillerat, A., Heinis, C., Correa, I.R. Jr., Kindermann, M., Beaufils, F., and Johnsson, K. (2008) An engineered protein tag for multiprotein labeling in living cells. Chem. Biol., 15, 128-136.
22. Giljohann, D.A., Seferos, D.S., Daniel, W.L., Massich, M.D., Patel, P.C., and Mirkin, C.A. (2010) Gold nanoparticles for biology and medicine. Angew. Chem. Int. Ed., 49, 3280-3294.
23. Glazer, A.N. (1989) Light guides directional energy transfer in a photosynthetic antenna. J. Biol. Chem., 264, 1-4.
24. de Graaf, A.J., Kooijman, M., Hennink, W.E., and Mastrobattista, E. (2009) Nonnatural amino acids for site-specific protein conjugation. Bioconjug. Chem., 20, 1281-1295.
25. Greenbaum, L., Rothmann, C., Lavie, R., and Malik, Z. (2000) Green fluorescent protein photobleaching: a model for protein damage by endogenous and exogenous singlet oxygen. Biol. Chem., 381, 1251-1258.
26. Griffin, B.A., Adams, S.R., and Tsien, R.Y. (1998) Specific covalent labeling of recombinant protein molecules inside live cells. Science, 281, 269-272.
27. Gronemeyer, T., Godin, G., and Johnsson, K. (2005) Adding value to fusion proteins through covalent labelling. Curr. Opin. Biotechnol., 16, 453-458.
28. 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, 461-465.
29. Habuchi, S., Ando, R., Dedecker, P., Verheijen, W., Mizuno, H., Miyawaki, A., and Hofkens, J. (2005) Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa. Proc. Natl. Acad. Sci. U.S.A., 102, 9511-9516.
30. Haraguchi, T. (2002) Live cell imaging: approaches for studying protein dynamics in living cells. Cell Struct. Funct., 27, 333-334.
31. Hardman, R. (2006) A toxicologic review of quantum dots: toxicity depends on physicochemical and environmental factors. Environ. Health Perspect., 114, 165-172.
32. Haugland, R.P. (2005) The Handbook-A Guide to Fluorescent Probes and Labeling Technologies, 10th edn, Molecular Probes, Eugene, OR.
33. Heim, R., Prasher, D.C., and Tsien, R.Y. (1994) Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. U.S.A., 91, 12501-12504.
34. Heiple, J.M. and Taylor, D.L. (1980) Intracellular pH in single motile cells. J. Cell Biol., 86, 885-890.
35. Henderson, J.N., Ai, H.W., Campbell, R.E., and Remington, S.J. (2007) Structural basis for reversible photobleaching of a green fluorescent protein homologue. Proc. Natl. Acad. Sci. U.S.A., 104, 6672-6677.
36. Henderson, J.N., Gepshtein, R., Heenan, J.R., Kallio, K., Huppert, D., and Remington, S.J. (2009) Structure and mechanism of the photoactivatable green fluorescent protein. J. Am. Chem. Soc., 131, 4176-4177.
37. Hermanson, G.T. (1996) Bioconjugate Techniques, Academic Press, San Diego, CA.
38. Heyes, C.D., Kobitski, A.Y., Breus, V.V., and Nienhaus, G.U. (2007) Effect of the shell on the blinking statistics of coreshell quantum dots: a single-particle fluorescence study. Phys. Rev. B, 75, 125431(125438 pages).
39. Hilderbrand, S.A. (2010) Labels and probes for live cell imaging: overview and selection guide. Methods Mol. Biol., 591, 17-45.
40. Hotz, C.Z. (2005) Applications of quantum dots in biology: an overview. Methods Mol. Biol., 303, 1-17.
41. Howarth, M., Liu, W., Puthenveetil, S., Zheng, Y., Marshall, L.F., Schmidt, M.M., Wittrup, K.D., Bawendi, M.G., and Ting, A.Y. (2008) Monovalent, reduced-size quantum dots for imaging receptors on living cells. Nat. Methods, 5, 397-399.
42. Huang, C.C., Yang, Z., Lee, K.H., and Chang, H.T. (2007) Synthesis of highly fluorescent gold nanoparticles for sensing mercury(II). Angew. Chem. Int. Ed., 46, 6824-6828.
43. Jares-Erijman, E.A. and Jovin, T.M. (2003) FRET imaging. Nat. Biotechnol., 21, 1387-1395.
44. Johnson, I.D. (2006) Practical considerations in the selection and application of fluorescent probes, in Handbook of Biological Confocal Microscopy (ed J.B. Pawley), Springer, New York.
45. Johnson, I. (2009) Fluorophores for optical imaging, in Optical Imaging of Cancer (eds E. Rosenthal and K.R. Zinn), Springer, New York.
46. Keppler, A., Pick, H., Arrivoli, C., Vogel, H., and Johnsson, K. (2004) Labeling of fusion proteins with synthetic fluorophores in live cells. Proc. Natl. Acad. Sci. U.S.A., 101, 9955-9959.
47. Kiick, K.L., Saxon, E., Tirrell, D.A., and Bertozzi, C.R. (2002) Incorporation of azides into recombinant proteins for chemoselective modification by the staudinger ligation. Proc. Natl. Acad. Sci. U.S.A., 99, 19-24.
48. Kim, H.D., Nienhaus, G.U., Ha, T., Orr, J.W., Williamson, J.R., and Chu, S. (2002) Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. U.S.A., 99, 4284-4289.
49. Labas, Y.A., Gurskaya, N.G., Yanushevich, Y.G., Fradkov, A.F., Lukyanov, K.A., Lukyanov, S.A., and Matz, M.V. (2002) Diversity and evolution of the green fluorescent protein family. Proc. Natl. Acad. Sci. U.S.A., 99, 4256-4261.
50. Lakowicz, J.R. (2006) Principles of Fluorescence Spectroscopy, 3rd edn, Springer, New York.
51. Lippincott-Schwartz, J., Snapp, E., and Kenworthy, A. (2001) Studying protein dynamics in living cells. Nat. Rev. Mol. Cell Biol., 2, 444-456.
52. Lovric, J., Cho, S.J., Winnik, F.M., and Maysinger, D. (2005) Unmodified cadmium telluride quantum dots induce reactive oxygen species formation leading to multiple organelle damage and cell death. Chem. Biol., 12, 1227-1234.
53. Lutty, G.A. (1978) The acute intravenous toxicity of biological stains, dyes, and other fluorescent substances. Toxicol. Appl. Pharmacol., 44, 225-249.
54. Magliery, T.J. and Regan, L. (2006) Reassembled GFP: detecting proteinprotein interactions and protein expression patterns. Methods Biochem. Anal., 47, 391-405.
55. Matz, M.V., Fradkov, A.F., Labas, Y.A., Savitsky, A.P., Zaraisky, A.G., Markelov, M.L., and Lukyanov, S.A. (1999) Fluorescent proteins from nonbioluminescent Anthozoa species. Nat. Biotechnol., 17, 969-973.
56. Michalet, X., Pinaud, F.F., Bentolila, L.A., Tsay, J.M., Doose, S., Li, J.J., Sundaresan, G., Wu, A.M., Gambhir, S.S., and Weiss, S. (2005) Quantum dots for live cells, in vivo imaging, and diagnostics. Science, 307, 538-544.
57. Miesenbock, G., De Angelis, D.A., and Rothman, J.E. (1998) Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins. Nature, 394, 192-195.
58. Nienhaus, G.U. (2006) Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromol. Biosci., 6, 907-922.
59. Nienhaus, G.U. (2008) The green fluorescent protein: a key tool to study chemical processes in living cells. Angew. Chem. Int. Ed., 47, 8992-8994.
60. Nienhaus, K., Nar, H., Heilker, R., Wiedenmann, J., and Nienhaus, G.U. (2008) Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611. J. Am. Chem. Soc., 130, 12578-12579.
61. Nienhaus, K., Nienhaus, G.U., Wiedenmann, J., and Nar, H. (2005) Structural basis for photo-induced protein cleavage and greento-red conversion of fluorescent protein EosFP. Proc. Natl. Acad. Sci. U.S.A., 102, 9156-9159.
62. Nienhaus, K., Vallone, B., Renzi, F., Wiedenmann, J., and Nienhaus, G.U. (2003) Crystallization and preliminary X-ray diffraction analysis of the red fluorescent protein eqFP611. Acta Crystallogr., Sect. D, 59, 1253-1255.
63. Noren, C.J., Anthony-Cahill, S.J., Griffith, M.C., and Schultz, P.G. (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science, 244, 182-188.
64. Oi, V.T., Glazer, A.N., and Stryer, L. (1982) Fluorescent phycobiliprotein conjugates for analyses of cells and molecules. J. Cell Biol., 93, 981-986.
65. Oswald, F., Schmitt, F., Leutenegger, A., Ivanchenko, S., D'Angelo, C., Salih, A., Maslakova, S., Bulina, M., Schirmbeck, R., Nienhaus, G.U. et al. (2007) Contributions of host and symbiont pigments to the coloration of reef corals. FEBS J., 274, 1102-1109.
66. Patterson, G.H. and Lippincott-Schwartz, J. (2002) A photoactivatable GFP for selective photolabeling of proteins and cells. Science, 297, 1873-1877.
67. Pegg, A.E. (2000) Repair of O(6)-alkylguanine by alkyltransferases. Mutat. Res., 462, 83-100.
68. Petersen, J., Wilmann, P.G., Beddoe, T., Oakley, A.J., Devenish, R.J., Prescott, M., and Rossjohn, J. (2003) The 2.0-A crystal structure of eqFP611, a far red fluorescent protein from the sea anemone Entacmaea quadricolor. J. Biol. Chem., 278, 44626-44631.
69. Pons, T. and Mattoussi, H. (2009) Investigating biological processes at the single molecule level using luminescent quantum dots. Ann. Biomed. Eng., 37, 1934-1959.
70. Reits, E.A. and Neefjes, J.J. (2001) From fixed to FRAP: measuring protein mobility and activity in living cells. Nat. Cell Biol., 3, E145-147.
71. Resch-Genger, U., Grabolle, M., Cavaliere-Jaricot, S., Nitschke, R., and Nann, T. (2008) Quantum dots versus organic dyes as fluorescent labels. Nat. Methods, 5, 763-775.
72. Rostovtsev, V.V., Green, L.G., Fokin, V.V., and Sharpless, K.B. (2002) A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective ligation of azides and terminal alkynes. Angew. Chem. Int. Ed., 41, 2596-2599.
73. Schuler, B. and Eaton, W.A. (2008) Protein folding studied by single-molecule FRET. Curr. Opin. Struct. Biol., 18, 16-26.
74. Schuler, B., Lipman, E.A., and Eaton, W.A. (2002) Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature, 419, 743-747.
75. Scorrano, L., Petronilli, V., Colonna, R., Di Lisa, F., and Bernardi, P. (1999) Chloromethyltetramethylrosamine (Mitotracker Orange) induces the mitochondrial permeability transition and inhibits respiratory complex I Implications for the mechanism of cytochrome c release. J. Biol. Chem., 274, 24657-24663.
76. Shagin, D.A., Barsova, E.V., Yanushevich, Y.G., Fradkov, A.F., Lukyanov, K.A., Labas, Y.A., Semenova, T.N., Ugalde, J.A., Meyers, A., Nunez, J.M. et al. (2004) GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity. Mol. Biol. Evol., 21, 841-850.
77. Shaner, N.C., Patterson, G.H., and Davidson, M.W. (2007) Advances in fluorescent protein technology. J. Cell Sci., 120, 4247-4260.
78. Shaner, N.C., Steinbach, P.A., and Tsien, R.Y. (2005) A guide to choosing fluorescent proteins. Nat. Methods, 2, 905-909.
79. Shu, X., Royant, A., Lin, M.Z., Aguilera, T.A., Lev-Ram, V., Steinbach, P.A., and Tsien, R.Y. (2009) Mammalian expression of infrared fluorescent proteins engineered from a bacterial phytochrome. Science, 324, 804-807.
80. Song, L., Varma, C.A., Verhoeven, J.W., and Tanke, H.J. (1996) Influence of the triplet excited state on the photobleaching kinetics of fluorescein in microscopy. Biophys. J., 70, 2959-2968.
81. Sperling, R.A., Rivera Gil, P., Zhang, F., Zanella, M., and Parak, W.J. (2008) Biological applications of gold nanoparticles. Chem. Soc. Rev., 37, 1896-1908.
82. Takahashi, A., Camacho, P., Lechleiter, J.D., and Herman, B. (1999) Measurement of intracellular calcium. Physiol. Rev., 79, 1089-1125.
83. Tsien, R.Y. (1998) The green fluorescent protein. Annu. Rev. Biochem., 67, 509-544.
84. Vogelsang, J., Kasper, R., Steinhauer, C., Person, B., Heilemann, M., Sauer, M., and Tinnefeld, P. (2008) A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angew. Chem. Int. Ed., 47, 5465-5469.
85. Wachter, R.M., Elsliger, M.A., Kallio, K., Hanson, G.T., and Remington, S.J. (1998) Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. Structure, 6, 1267-1277.
86. Wallrabe, H. and Periasamy, A. (2005) Imaging protein molecules using FRET and FLIM microscopy. Curr. Opin. Biotechnol., 16, 19-27.
87. Wang, L., Brock, A., Herberich, B., and Schultz, P.G. (2001) Expanding the genetic code of Escherichia coli. Science, 292, 498-500.
88. Wang, Y., Shyy, J.Y., and Chien, S. (2008) Fluorescence proteins, live-cell imaging, and mechanobiology: seeing is believing. Annu. Rev. Biomed. Eng., 10, 1-38.
89. Warner, J.H., Hoshino, A., Yamamoto, K., and Tilley, R.D. (2005) Water-soluble photoluminescent silicon quantum dots. Angew. Chem. Int. Ed., 44, 4550-4554.
90. Wiedenmann, J., Elke, C., Spindler, K.D., and Funke, W. (2000) Cracks in the betacan: fluorescent proteins from anemonia sulcata (Anthozoa, Actinaria). Proc. Natl. Acad. Sci. U.S.A., 97, 14091-14096.
91. Wiedenmann, J., Ivanchenko, S., Oswald, F., Schmitt, F., Röcker, 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, 15905-15910.
92. Wiedenmann, J. and Nienhaus, G.U. (2006) Live-cell imaging with EosFP and other photoactivatable marker proteins of the GFP family. Expert Rev. Proteomics, 3, 361-374.
93. Yin, J., Liu, F., Li, X., and Walsh, C.T. (2004) Labeling proteins with small molecules by site-specific posttranslational modification. J. Am. Chem. Soc., 126, 7754-7755.
94. Zhang, J., Campbell, R.E., Ting, A.Y., and Tsien, R.Y. (2002) Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol., 3, 906-918.