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Fluorophore Literature References

A wide spectrum of synthetic fluorophores and hybrid systems composed of genetically-encoded targets and membrane permeable tags have been developed for imaging living and fixed cells. Among the most useful synthetics are the Alexa Fluors, Cyanine (Cy series) dyes, ATTO dyes, and Tracker series. Hybrid systems rely on targeting a genetically-encoded receptor using a membrane-permeable synthetic fluorophore and are best exemplified by the FlAsH system.

Additional Literature Sources

Bagshaw, C. R. and Cherny, D. Blinking fluorophores: what do they tell us about protein dynamics? Biochemical Society Transactions 34: 979- 982 (2006).
Baruah, H., Puthenveetil, S., Choi, Y. A., Shah, S. and Ting, A. Y. An engineered aryl azide ligase for site-specific mapping of protein-protein interactions through photo-cross-linking. Angewandte Chemie 47: 7018- 7021 (2008).
Buschmann, V., Weston, K. D. and Sauer, M. Spectroscopic study and evaluation of red-absorbing fluorescent dyes. Bioconjugate Chemistry 14: 195-204 (2003).
Chen, I., Howarth, M., Lin, W. and Ting, A. Y. Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nature Methods 2: 99-104 (2005).
Chin, J. W. An expanded eukaryotic genetic code. Science 301: 964- 967(2003).
Clarkson, T., Yang, W., Rozamus, L. W., Hatada, M., Amara, J. F., Rollins, C. T., Stevenson, L. F., Magari, S. R., Wood, S. A., Courage, N. L., Lu, X., Cerasoli Jr., F., Gilman, M. and Holt, D. A. Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity. Proceedings of the National Academy of Sciences (USA) 95: 10437-10443 (1998).
Conley, N. R., Biteen, J. S. and Moerner, W. E. Cy3-Cy5 covalent heterodimers for single-molecule photoswitching. Journal of Physical Chemistry 112: 11878-11880 (2008).
Daly, C. J. and McGrath, J. C. Fluorescent ligands, antibodies, and proteins for the study of receptors. Pharmacology and Therapeutics 100: 101-118 (2003).
Eisenstein, M. Helping cells to tell a colorful tale. Nature Methods 3: 647-655 (2006).
Erve, A., Saoudi, Y., Thirot, S., Guetta-Landras, C., Florent, J. C., Nguyen, C. H., Grierson, D. S. and Popov, A. V. BENA435, a new cell-permeant photoactivated green fluorescent DNA probe. Nucleic acids research 34: 43 (2006).
Evanko, D. The new fluorescent probes on the block. Nature Methods 5: 218-219 (2008).
Famulok, M. Green Fluorescent RNA. Nature 430: 976-977 (2004).
Fernandez-Suarez, M., Baruah, H., Martinez-Hernandez, L., Xie, K. T., Baskin, J. M., Bertozzi, C. R. and Ting, A. Y. Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes. Nature Biotechnology 25: 1483-1487 (2007).
Flors, C., Fryer, M. J., Waring, J., Reeder, B., Bechtold, U., Mullineaux, P. M., Nonell, S., Wilson, M. T. and Baker, N. R. Imaging the production of singlet oxygen in vivo using a new fluorescent sensor, singlet oxygen sensor green. Journal of Experimental Botany 57: 1725-1734 (2006).
Freundt, E. C., Czapiga, M. and Lenardo, M. J. Photoconversion of Lysotracker Red to a green fluorescent molecule. Cell Research 17: 956-958 (2007).
Fukaminato, T., Umemoto, T., Iwata, Y., Yokojima, S., Yoneyama, M., Nakamura, S. and Irie, M. Photochromism of diarylethene single molecules in polymer matrices. Journal of the American Chemical Society 129: 5932-5938 (2007).
Gee, K. R., Weinberg, E. S. and Kozlowski, D. J. Caged Q-rhodamine dextran: a new photoactivated fluorescent tracer. Bioorganic and Medicinal Chemistry Letters 11: 2181-2183 (2001).
Gendreizig, S., Kindermann, M. and Johnsson, K. Induced protein dimerization in vivo through covalent labeling. Journal of the American Chemical Society 125: 14970-14971 (2003).
George, N., Pick, H., Vogel, H., Johnsson, N. and Johnson, K. Specific labeling of cell surface proteins with chemically diverse compounds. Journal of the American Chemical Society 126: 8896-8897 (2004).
Grinvald, A. and Hildesheim, R. VSDI: A new era in functional imaging of cortical dynamics. Nature Reviews Neuroscience 5: 874-885 (2004).
Gruber, H. J., Hahn, C. D., Kada, G., Riener, C. K., Harms, G. S., Ahrer, W., Dax, T. G. and Knaus, H. G. Anomalous fluorescence enhancement of Cy3 and Cy3.5 versus anomalous fluorescence loss of Cy5 and Cy7 upon covalent linking to IgG and noncovalent binding to avidin. Bioconjugate Chemistry 11: 696-704 (2000).
Guignet, E. G., Hovius, R. and Vogel, H. Reversible site-selective labeling of membrane proteins in live cells. Nature Biotechnology 22: 440-444 (2004).
Hauser, C. T. and Tsien, R. Y. A hexahistidine-Zn2+-dye label reveals STIM1 surface exposure. Proceedings of the National Academy of Sciences (USA) 104: 3693-3697 (2007).
Honda, K., Nakata, E., Ojida, A. and Hamachi, I. Ratiometric fluorescence detection of a tag fused protein using the dual-emission artificial molecular probe. Chemical Communications 2006: 4024-4026 (2006).
Howarth, M., Chinnapen, D. J. F., Gerrow, K., Dorrestein, P. C., Grandy, M. R., Kelleher, N. L., El-Husseini, A. and Ting, A. Y. A monovalent streptavidin with a single femtomolar biotin binding site. Nature Methods 3: 267-273 (2006).
Juillerat, A., Gronemeyer, T., Keppler, A., Gengreizig, S., Pick, H., Vogel, H. and Johnsson, K. Directed evolution of O6-alkylguanine-DNA alkyltransferase for efficient labeling of fusion proteins with small molecules in vivo. Chemistry and Biology 10: 313-317 (2003).
Juillerat, A., Heinis, C., Sielaff, I., Barnikow, J., Jaccard, H., Kunz, B., Terskikh, A. and Johnsson, K. Engineering substrate specificity of O6- alkylguanine-DNA alkyltransferase for specific protein labeling in living cells. ChemBioChem 6: 1263-1269 (2005).
Keppler, A., Kindermann, M., Gendreizig, S., Pick, H., Vogel, H. and Johnsson, K. Labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase with small molecules in vivo and in vitro. Methods 32: 437-444 (2004).
Kindermann, M., George, N., Johnsson, N. and Johnsson, K. Covalent and selective immobilization of fusion proteins. Journal of the American Chemical Society 125: 7810-7811 (2003).
Kindermann, M., Sielaff, I. and Johnsson, K. Synthesis and characterization of bifunctional probes for the specific labeling of fusion proteins. Bioorganic and Medicinal Chemistry Letters 14: 2725-2728 (2004).
Kuhn, B., Fromherz, P. and Denk, W. High sensitivity of stark-shift voltage-sensing dyes by one- or two-photon excitation near the red spectral edge. Biophysical Journal 87: 631-639 (2004).
Lata, S., Gavutis, M., Tamp, R. and Piehler, J. Specific and stable fluorescence labeling of histidine-tagged proteins for dissecting multi-protein complex formation. Journal of the American Chemical Society 128: 2365- 2372 (2006).
Lin, C. W. and Ting, A. Y. Transglutaminase-catalyzed site-specific conjugation of small-molecule probes to proteins in vitro and on the surface of living cells. Journal of the American Chemical Society 128: 4542-4543 (2006).
Lord, S. J., Conley, N. R., Lee, H. L. D., Samuel, R., Liu, N., Twieg, R. J. and Moerner, W. E. A photoactivatable push-pull fluorophore for single-molecule imaging in live cells. Journal of the American Chemical Society 130: 9204-9205 (2008).
Marks, K. M., Braun, P. D. and Nolan, G. P. A general approach for chemical labeling and rapid, spatially controlled protein inactivation. Proceedings of the National Academy of Sciences (USA) 101: 9982-9987 (2004).
Marks, K. M., Rosinov, M. and Nolan, G. P. In vivo targeting of organic calcium sensors via genetically selected peptides. Chemistry and Biology 11: 347-356 (2004).
Martin, R. M., Leonhardt, H. and Cardoso, M. C. DNA labeling in living cells. Cytometry 67A: 45-52 (2005).
Meiblitzer-Ruppitsch, C., Vetterlein, M., Stangl, H., Maier, S., Neumuller, J., Freismuth, M., Pavelka, M. and Ellinger, A. Electron microscopic visualization of fluorescent signals in cellular compartments and organelles by means of DAB-photoconversion. Histochemistry and Cell Biology 130: 407-419 (2008).
Miller, L. W., Cai, Y., Sheetz, M. P. and Cornish, V. W. In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag. Nature Methods 2: 255-257 (2005).
Miller, L. W., Sable, J., Goelet, P., Sheetz, M. P. and Cornish, V. W. Methotrexate conjugates: A molecular in vivo protein tag Angewandte Chemie 43: 1672- 1675 (2004).
Mujumdar, R. B., Ernst, L. A., Mujumdar, S. R., Lewis, C. J. and Waggoner, A. S. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjugate Chemistry 4: 105-111 (1993).
Nakanishi, J., Nakajima, T., Sato, M., Ozawa, T., Tohda, K. and Umezawa, Y. Imaging of conformational changes of proteins with a new environment-sensitive fluorescent probe designed for site-specific labeling of recombinant proteins in live cells. Analytical Chemistry 73: 2920-2928 (2001).
Neef, A. B. and Schultz, C. Selective fluorescence labeling of lipids in living cells. Angewandte Chemie 48: 1498- 1500 (2009).
Nonaka, H., Tsukiji, S., Ojida, A. and Hamachi, I. Non-enzymatic covalent protein, labeling using a reactive tag. Journal of the American Chemical Society 129: 15777-15779 (2007).
Ohmichi, T., Kawamoto, Y., Wu, P., Miyoshyi, D., Karimata, H. and Sugimoto, N. DNA-based biosensor for monitoring pH in vitro and in living cells. Biochemistry 44: 7125-7130 (2005).
Ojida, A., Honda, K., Shinmi, D., Kiyonaka, S., Mori, Y. and Hamachi, I. Oligo-Asp Tag/Zn(II) complex probe as a new pair for labeling and fluorescence imaging of proteins. Journal of the American Chemical Society 128: 10452-10459 (2006).
Patsenker, L., Tatarets, A., Kolosova, O., Obukhova, O., Povrozin, Y., Fedyunyayeva, I., Yermolenko, I. and Terpetschnig, E. Fluorescent probes and labels for biomedical applications. Annals of the New York Academy of Sciences 1130: 179-187 (2008).
Popp, M. W., Antos, J. M., Grotenbreg, G. M., Spooner, E. and Ploegh, H. L. Sortagging: a versatile method for protein labeling. Nature Chemical Biology 3: 707-708 (2007).
Prescher, J. A. and Bertozzi, C. R. Chemistry in living systems. Nature Chemical Biology 1: 13-21 (2005).
Remy, I. and Michnick, S. W. Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. Proceedings of the National Academy of Sciences (USA) 96: 5394-5399 (1999).
Riedl, J., Crevenna, A. H., Kessenbrock, K., Yu, J. H., Neukirchen D., Bista, M., Bradke, F., Jenne, D., Holak, T. A., Werb, Z., Sixt, M. and Wedlich-Soldner, R. Lifeact: a versatile marker to visualize F-actin. Nature Methods 5: 605-607 (2008).
Rigler, P. and Meier, W. Encapsulation of fluorescent molecules by functionalized polymeric nanocontainers: investigation by confocal fluorescence imaging and fluorescence correlation spectroscopy. Journal of the American Chemical Society 128: 367-373 (2006).
Roberti, M. J., Bertoncini, C. W., Klement, R., Jares-Erijman, E. A. and Jovin, T. M. Fluorescence imaging of amyloid formation in living cells by a functional, tetracysteine-tagged α-synuclein. Nature Methods 4: (2007).
Rozinov, M. N. and Nolan, G. P. Evolution of peptides that modulate the spectral qualities of bound, small-molecule fluorophores. Chemistry and Biology 5: 713-728 (1998).
Schmued, L. C. and Hopkins, K. J. Fluoro-jade B: a high affinity fluorescent marker for the localization of neuronal degeneration. Brain Research 874: 123-130 (2000).
Smith, P. J., Blunt, N., Wiltshire, M., Hoy, T., Teesdale-Spittle, P., Craven, M. R., Watson, J. V., Amos, W. B., Errington, R. J. and Patterson, L. H. Characteristics of a novel deep red-infrared fluorescent cell-permeant DNA probe, DRAQ5, in intact human cells analyzed by flow cytometry, confocal and multiphoton microscopy. Cytometry 40: 280-291 (2000).
Suzuki, T., Matsuzaki, T., Hagiwara, H., Aoki, T. and Takata, K. Recent advances in fluorescent labeling techniques for fluorescence microscopy. Japan Society of Histochemistry and Cytochemistry 40: 131-137 (2007).
Szent-Gyorgyi, C., Schmidt, B. A., Creeger, Y., Fisher, G. W., Zakel, K. L., Adler, S., Fitzpatrick, J. A. J., Woolford, C. A., Yan, Q., Vasilev, K. V., Berget, P. B., Bruchez, M. P., Jarvik, J. W. and Waggoner, A. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nature Biotechnology 26: 235- 240 (2008).
Tanaka, T., Yamamoto, T., Tsukiji, S. and Nagamune, T. Site-specific protein modification on living cells catalyzed by sortase. ChemBioChem 9: 802-807 (2008).
van Zandvoort, M. A. M. J., de Grauw, C. J., Gerritsen, H. C., Broers, J. L. V., Egbrink, M. G. A. O., Ramaekers, F. C. S. and Slaaf, D. W. Discrimination of DNA and RNA in cells by a vital fluorescent probe: lifetime imaging of SYTO13 in healthy and apoptotic cells. Cytometry 47: 226-235 (2002).
Vercelli, A., Repici, M., Garbossa, D. and Grimaldi, A. Recent techniques for tracing pathways in the central nervous system of developing and adult mammals. Brain Research Bulletin 51: 11-28 (2000).
Vivero-Pol, L., George, N., Krumm, H., Johnsson, K. and Johnsson, N. Multicolor imaging of cell surface proteins. Journal of the American Chemical Society 127: 12770-12771 (2005).
Wang, L. Expanding the genetic code of Escherichia coli. Science 292: 498-500 (2001).
Weissleder, R. A clearer vision for in vivo imaging. Nature Biotechnology 19: 316-317 (2001).
Weissleder, R. and Ntziachristos, V. Shedding light onto live molecular targets. Nature Medicine 9: 123-128 (2003).
Wu, M. M., Llopis, J., Adams, S., McCaffery, J. M., Kulomaa, M. S., Machen, T. E., Moore, H. P. H. and Tsien, R. Y. Organelle pH studies using targeted avidin and fluorescein-biotin. Chemistry and Biology 7: 197-209 (2000).
Yeo, D. S. Y., Srinivasan, R., Uttamchandani, M., Chen, G. Y. J., Zhu, Q. and Yao, S. Q. Cell-permeable small molecule probes for site-specific labeling of proteins. Chemical Communications 23: 2870-2871 (2003).
Yin, J., Liu, F., Li, X. and Walsh, C. T. Labeling proteins with small molecules by site-specific posttranslational modification. Journal of the American Chemical Society 126: 7754-7755 (2004).
Zhang, Z., Alfonta, L., Tian, F., Bursulaya, B., Uryu, S., King, D. S. and Schultz, P. G. Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells. Proceedings of the National Academy of Sciences (USA) 101: 8882-8887 (2004).
Zhou, Z., Cironi, P., Lin, A. J., Xu Y., Hrvatin, S., Golan, D. E., Silver, P. A., Walsh, C. T. and Yin, J. Genetically encoded short peptide tags for orthogonal protein labeling by SFp and AcpS phosphopantetheinyl transferases. ACS Chemical Biology 2: 337-346 (2007).

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