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Applications in Confocal Microscopy
Fluorescent Protein Literature Sources
The disciplines of cellular and molecular biology are being rapidly and dramatically transformed by the application of fluorescent proteins developed from marine organisms as fusion tags to track protein behavior in living cells. The most widely used of these probes, green fluorescent protein, can be attached to virtually any target of interest and still fold into a viable fluorescent species. The resulting chimera can be employed to localize previously uncharacterized proteins or to visualize and track known proteins to further understand critical events at the cellular and molecular levels. This section features a bibliography of literature sources for review articles and original research reports on the discovery, applications, and continued development of fluorescent proteins.
Abad, M. F. C., Benedetto, G. D., Magalhăes, P. J., Filippin, L., and Pozzan, T., Mitochondrial pH monitored by a new engineered green fluorescent protein mutant., Journal of Biological Chemistry 279: 11521-11529 (2004). | PubMed |
Abedi, M. R., Caponigro, G., and Kamb, A., Green fluorescent protein as a scaffold for intracellular presentation of peptides., Nucleic Acids Research 26: 623-630 (1998).
| PubMed |
Adams, S. R., Kao, J. P. Y., Grynkiewicz, G., Minta, A., and Tsien, R. Y., Biologically useful chelators that release calcium upon illumination., Journal of the American Chemical Society 110: 3212-3220 (1988). | JACS |
Akemann, W., Raj, C. D., and Knöpfel, T., Functional characterization of permuted enhanced green fluorescent proteins comprising varying linker peptides., Photochemistry and Photobiology 74: 356-363 (2001). | PubMed |
Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H., and Miyawaki, A., An optical marker based on the UV-induced green-to-red-photoconversion of a fluorescent protein., Proceedings of the National Academy of Sciences (USA) 99: 12651-12656 (2002).
| PubMed |
Ando, R., Mizuno, H., and Miyawaki, A., Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting., Science 306: 1370-1373 (2004).
| PubMed |
Arimura, S., Yamamoto, J., Aida, G. P., Nakazono, M., and Tsutsumi, N., Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution., Proceedings of the National Academy of Sciences (USA) 101: 7805-7808 (2004). | PubMed |
Ataka, K. and Pieribone, V. A., A genetically targetable fluorescent probe of channel gating with rapid kinetics., Biophysical Journal 82: 509-516 (2002). | PubMed |
Bae, J. H., Pal, P. P., Moroder, L., Huber, R., and Budisa, N., Crystallographic evidence for isomeric chromophores in 3-fluorotyrosyl-green fluorescent protein., ChemBioChem 5: 720-722 (2004). | PubMed |
Bae, J. H., Rubini, M., Jung, G., Wiegand, G., Seifert, M. H. J., Azim, M. K., Kim, J.-S., Zumbusch, A., Holak, T. A., Moroder, L., Huber, R., and Budisa, N., Expansion of the genetic code enables design of a novel "gold" class of green fluorescent proteins., Journal of Molecular Biology 328: 1071-1081 (2003). | PubMed |
Baird, G. S., Zacharias, D. A., and Tsien, R. Y., Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral., Proceedings of the National Academy of Sciences (USA) 97: 11984-11989 (2000). | PubMed |
Baird, G. S., Zacharias, D. A., and Tsien, R. Y., Circular permutation and receptor insertion within green fluorescent proteins., Proceedings of the National Academy of Sciences (USA) 96: 11241-11246 (1999). | PubMed |
Baldini, G., Cannone, F., and Chirico, G., Pre-unfolding resonant oscillations of single green fluorescent protein molecules., Science 309: 1096-100 (2005). | PubMed |
Barondeau, D. P., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D., Structural chemistry of a green fluorescent protein Zn biosensor., Journal of the American Chemical Society 124: 3522-3524 (2002). | PubMed |
Barondeau, D. P., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D., Understanding GFP chromophore biosynthesis: Controlling backbone cyclization and modifying post-translational chemistry., Biochemistry 44: 1960-1970 (2005). | PubMed |
Barondeau, D. P., Putnam, C. D., Kassmann, C. J., Talner, J. A., and Getzoff, E. D., Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures., Proceedings of the National Academy of Sciences (USA) 100: 12111-12116 (2003). | PubMed |
Bates, M., Blosser, T. R., and Zhuang, X., Short-range spectroscopic ruler based on a single-molecule optical switch., Physical Review Letters 94: 108101 (2005). | PRL |
Battistutta, R., Negro, A., and Zanotti, G., Crystal structure and refolding properties of the mutant F99S/M153T/V163A of the green fluorescent protein., Proteins: Structure, Function, and Genetics 41: 429-437 (2000). | PubMed |
Beddoe, T., Ling, M., Dove, S., Hoegh-Guldberg, O., Devenish, R., Prescott, M., and Rossjohn, J., The production, purification and crystallization of a pocilloporin pigment from a reef-forming coral., Acta Crystallographica, Section D: Biological Crystallography 59: 597-599 (2003). | AC |
Bell, A. F., He, X., Wachter, R. M., and Tonge, P. J., Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy., Biochemistry 39: 4423-4431 (2000). | PubMed |
Bell, A. F., Stoner-Ma, D., Wachter, R. M., and Tonge, P. J., Light-driven decarboxylation of wild-type green fluorescent protein., Journal of the American Chemical Society 125: 6919-6926 (2003). | PubMed |
Belmont, A. S., Visualizing chromosome dynamics with GFP., Trends in Cell Biology 11: 250-257 (2001). | PubMed |
Berridge, M. J., Lipp, P., and Bootman, M. D., The versatility and universality of calcium signaling., Nature Reviews Molecular Cell Biology 1: 11-21 (2000). | PubMed |
Bevis, B. J. and Glick, B. S., Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed)., Nature Biotechnology 20: 83-87 (2002). | PubMed |
Billinton, N. and Knight, A. W., Seeing the wood through the trees: A review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence., Analytical Biochemistry 291: 175-197 (2001). | PubMed |
Biondi, R. M., Baehler, P. J., Reymond, C. D., and Véron, M., Random insertion of GFP into the cAMP-dependent protein kinase regulatory subunit from Dictyostelium discoideum., Nucleic Acids Research 26: 4946-4952 (1998). | PubMed |
Blab, G. A., Lommerse, P. H. M., Cognet, L., Harms, G. S., and Schmidt, T., Two-photon excitation action cross-sections of the autofluorescent proteins., Chemical Physics Letters 350: 71-77 (2001). | CPL |
Bongaerts, J. M., Hautefort, I., Sidebotham, J. M., and Hinton, J. C. D., Green fluorescent protein as a marker for conditional gene expression in bacterial cells., Methods in Enzymology 358: 43-66 (2002). | PubMed |
Bonsma, S., Purchase, R., Jezowksi, S., Gallus, J., Könz, F., and Völker, S., Green and red fluorescent proteins: Photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning., ChemPhysChem 6: 838-849 (2005).
| PubMed |
Bowen, B. and Woodbury, N., Single-molecule fluorescence lifetime and anisotropy measurements of the red fluorescent protein, DsRed, in solution., Photochemistry and Photobiology 77: 362-69 (2003). | PubMed |
Branchini, B. R., Nemser, A. R., and Zimmer, M., A computational analysis of the unique protein-induced tight turn that results in posttranslational chromophore formation in green fluorescent protein., Journal of the American Chemical Society 120: 1-6 (1998).
| JACS |
Brandizzi, F., Fricker, M., and Hawes, C., A greener world: The revolution in plant bioimaging., Nature Reviews Molecular and Cell Biology 3: 520-530 (2002). | PubMed |
Brejc, K., Sixma, T., Kitts, P. A., Kain, S. R., Tsien, R. Y., Ormo, M., and Remington, S. J., Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein., Proceedings of the National Academy of Sciences (USA) 94: 2306-2311 (1997). | PubMed |
Brooks, S., The discovery of aequorin and green fluorescent protein., Journal of Microscopy 217: 1-2 (2005). | PubMed |
Bublitz, G., King, B. A., and Boxer, S. G., Electronic structure of the chromophore in green fluorescent protein (GFP)., Journal of the American Chemical Society 120: 9370-9371 (1998). | JACS |
Budisa, N., Pal, P. P., Alefelder, S., Birle, P., Krywcun, T., Rubini, M., Wenger, W., Bae, J. H., and Steiner, T., Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code., Biological Chemistry 385: 191-202 (2004).
| PubMed |
Bulina, M. E., Chudakov, D. M., Mudrik, N. N., and Lukyanov, K. A., Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis., BMC Biochemistry 3: 7 (2002). | PubMed |
Bulina, M. E., Lukyanov, K. A., Yampolsky, I. V., Chudakov, D. M., Staroverov, D. B., Shcheglov, A. S., Gurskaya, N. G., and Lukyanov, S., New class of blue animal pigments based on frizzled and kringle protein domains., Journal of Biological Chemistry 279: 43367-43370 (2004). | PubMed |
Bulina, M. E., Verkhusha, V. V., Staroverov, D. B., Chudakov, D. M., and Lukyanov, K. A., Hetero-oligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteins., Biochemical Journal 371: 109-114 (2003).
| PubMed |
Cabantous, S., Terwilliger, T. C., and Waldo, G. S., Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein., Nature Biotechnology 23: 102-107 (2005). | PubMed |
Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., and Tsien, R. Y., A monomeric red fluorescent protein., Proceedings of the National Academy of Sciences (USA) 99: 7877-7882 (2002). | PubMed |
Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., and Prasher, D. C., Green fluorescent protein as a marker for gene expression., Science 263: 802-805 (1994). | PubMed |
Chamberlain, C. and Hahn, K. M., Watching proteins in the wild: Fluorescence methods to study protein dynamics in living cells., Traffic 1: 755-762 (2000). | PubMed |
Chattoraj, M., King, B. A., Bublitz, G. U., and Boxer, S. G., Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer., Proceedings of the National Academy of Sciences (USA) 93: 8362-8367 (1996). | PubMed |
Chen, Y., Mills, J. D., and Periasamy, A., Protein localization in living cells and tissues using FRET and FLIM., Differentiation 71: 528-541 (2003). | PubMed |
Cheng, L., Fu, J., Tsukamoto, A., and Hawley, R. G., Use of green fluorescent protein variants to monitor gene transfer and expression in mammalian cells., Nature Biotechnology 14: 606-609 (1996). | PubMed |
Chudakov, D. M., Belousov, V. V., Zaraisky, A. G., Novoselov, V. V., Staroverov, D. B., Zorov, D. B., Lukyanov, S., and Lukyanov, K. A., Kindling fluorescent proteins for precise in vivo photolabeling., Nature Biotechnology 21: 191-194 (2003). | PubMed |
Chudakov, D. M., Feofanov, A. V., Mudrik, N. N., Lukyanov, S., and Lukyanov, K. A., Chromophore environment provides clues to "kindling fluorescent protein" riddle., Journal of Biological Chemistry., 278: 7215-7219 (2003). | PubMed |
Chudakov, D. M. and Lukyanov, K. A., Use of green fluorescent protein (GFP) and its homologs for in vivo protein motility studies., Biochemistry (Moscow) 68: 952-957 (2003). | PubMed |
Chudakov, D. M., Verkhusha, V. V., Staroverov, D. B., Souslova, E. A., Lukyanov, S., and Lukyanov, K. A., Photoswitchable cyan fluorescent protein for protein tracking., Nature Biotechnology 22: 1435-1439 (2004). | PubMed |Cinelli, R. A. G., Ferrari, A., Pellegrini, V., Signorelli, A., Tyagi, M., Giacca, M., and Beltram, F., Engineering single-molecule fluorescence dynamics for advanced biomolecular applications., Australian Journal of Chemistry 54: 107-111 (2001). | AJC |
Cinelli, R. A. G., Pellegrini, V., Ferrari, A., Faraci, P., Nifosi, R., Tyagi, M., Giacca, M., and Beltram, F., Green fluorescent proteins as optically controllable elements in bioelectronics., Applied Physics Letters 79: 3353-3355 (2001). | APL |
Cody, C. W., Prahser, D. C., Westler, W. M., Prendergast, F. G., and Ward, W. W., Chemical structure of the hexapeptide chromophore Aequorea green-fluorescent protein., Biochemistry 32: 1212-1218 (1993). | PubMed |
Cormack, B. P., Valdivia, R. H., and Falkow, S., FACS-optimized mutants of the green fluorescent protein (GFP)., Gene 173: 33-38 (1996). | PubMed |
Cotlet, M., Hofkens, J., Habuchi, S., Dirix, G., Van Guyse, M., Michiels, J., Vanderleyden, J., and De Schryver, F. C., Identification of different emitting species in the red fluorescent protein DsRed by means of ensemble and single-molecule spectroscopy., Proceedings of the National Academy of Sciences (USA) 98: 14398-14403 (2001).
| PubMed |
Cotlet, M., Hofkens, J., Köhn, F., Michiels, J., Dirix, G., Van Guyse, M., Vanderleyden, J., and De Schryver, F. C., Collective effects in individual oligomers of the red fluorescent coral protein DsRed., Chemical Physics Letters 336: 415-423 (2001). | CPL |
Cotlet, M., Hofkens, J., Maus, M., Gensch, T., Van der Auweraer, M., Michiels, J., Dirix, G., Van Guyse, M., Vanderleyden, J., Visser, A. J. W. G., and De Scheyver, F. C., Excited-state dynamics in the enhanced green fluorescent protein mutant probed by picosecond time-resolved single photon counting spectroscopy., Journal of Physical Chemistry B 105: 4999-5006 (2001). | JPCB |
Cox, G. and Salih, A., Fluorescence lifetime imaging of symbionts and fluorescent proteins in reef corals., Proceedings of the International Society for Optical Engineering (SPIE) 5700: 162-170 (2005). | SPIE |
Crameri, A., Whitehorn, E. A., Tate, E., and Stemmer, W. P. C., Improved green fluorescent protein by molecular evolution using DNA shuffling., Nature Biotechnology 14: 315-319 (1996). | PubMed |
Creemers, T. M. H., Lock, A. J., Subramanium, V., Jovin, T. M., and Volker, S., Three photoconvertible forms of green fluorescent protein identified by spectral hole-burning., Nature Structural Biology 6: 557-560 (1999). | PubMed |
Cubitt, A. B., Heim, R., Adams, S. R., Boyd, A. E., Gross, L. A., and Tsien, R. Y., Understanding, improving and using green fluorescent proteins., Trends in Biochemical Sciences 20: 448-455 (1995). | PubMed |
Dandekar, D. H., Kumar, M., Ladha, J. S., Ganesh, K. N., and Mitra, D., A quantitative method for normalization of transfection efficiency using enhanced green fluorescent protein., Analytical Biochemistry 342: 341-344 (2005). | PubMed |
Delagrave, S., Hawtin, R. E., Silva, C. M., Yang, M. M., and Youvan, D. C., Red-shifted excitation mutants of the green fluorescent protein., Nature Biotechnology 13: 151-154 (1995). | PubMed |
Demaurex, N. and Frieden, M., Measurements of the free luminal ER calcium concentration with targeted "chameleon" fluorescent proteins., Cell Calcium 34: 109-119 (2003). | PubMed |
Deryusheva, S. and Gall, J. G., Dynamics of coilin in Cajal bodies of the Xenopus germinal vesicle., Proceedings of the National Academy of Sciences (USA) 101: 4810-4814 (2004). | PubMed |
Dickson, R. M., Cubitt, A. B., Tsien, R. Y., and Moerner, W. E., On/off blinking and switching behavior of single molecules of green fluorescent protein., Nature 388: 355-358 (1997). | PubMed |
Dooley, C. T., Dore, T. M., Hanson, G. T., Jackson, W. C., Remington, S. J., and Tsien, R. Y., Imaging dynamic redox changes in mammalian cells with green fluorescent protein indicators., Journal of Biological Chemistry 279: 22284-22293 (2004). | PubMed |
Dopf, J. and Horiagon, T. M., Deletion mapping of the Aequorea victoria green fluorescent protein., Gene 173: 39-44 (1996). | PubMed |
Dove, S. G., Hoegh-Guldberg, O., and Ranganathan, S., Major colour patterns of reef-building corals are due to a family of GFP-like proteins., Coral Reefs 19: 197-204 (2001). | Coral Reefs |
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Dundr, M., McNally, J. G., Cohen, J., and Misteli, T., Quantitation of GFP-fusion proteins in single living cells., Journal Structural Biology 140: 92-99 (2002a). | PubMed |
Ehrhardt, D., GFP technology for live cell imaging., Current Opinion in Plant Biology 6: 622-628 (2003). | PubMed |
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Eisenstein, M., A better way to pick a plum., Nature Methods 2: 87 (2005). | Nat Methods |
Eisenstein, M., New fluorescent protein includes handy on-off switch., Nature Methods 2: 8-9 (2005). | Nat Methods |
Ellenberg, J., Lippincott-Schwartz, J., and Presley, J. F., Dual-colour imaging with GFP variants., Trends in Cell Biology 9: 52-56 (1999). | PubMed |
Ellenberg, J., Lippincott-Schwartz, J., and Presley, J. F., Two-color green fluorescent protein time-lapse imaging., BioTechniques 25: 838-846 (1998). | PubMed |
Elowitz, M. B., Surette, M. G., Wolf, P.-E., Stock, J. B., and Leibler, S., Photoactivation turns green fluorescent protein red., Current Biology 7: 809-812 (1997). | PubMed |
Elowitz, M. B., Surette, M. G., Wolf, P.-E., Stock, J. B., and Leibler, S., Protein mobility in the cytoplasm of Escherichia coli., Journal of Bacteriology 181: 197-203 (1999). | PubMed |
Elsiger, M.-A., Wachter, R. M., Hanson, G. T., Kallio, K., and Remington, S. J., Structural and spectral response of green fluorescent protein variants to changes in pH., Biochemistry 38: 5296-5301 (1999). | PubMed |
Erickson, M. G., Alseikhan, B. A., Peterson, B. Z., and Yue, D. T., Preassociation of calmodulin with voltage-gated calcium channels revealed by FRET in single living cells., Neuron 31: 973-985 (2001). | PubMed |
Evanko, D., Highlighting protein movement in living cells., Nature Methods 1: 96-97 (2004). | Nat Methods |
Fehr, M., Okumoto, S., Deuschle, K., Lager, I., Looger, L. L., Persson, J., Kozhuhk, L., Lalonde, S., and Frommer, W. B., Development and use of fluorescent nanosensors for metabolite imaging in living cells., Biochemical Society Transactions 33: 287-290 (2005). | PubMed |
Fiala, A., Spall, T., Diegelmann, S., Eisermann, B., Sachse, S., Devaud, J.-M., Buchner, E., and Galizia, C. G., Genetically expressed cameleon in Drosophila melanogaster is used to visualize olfactory information in projection neurons., Current Biology 12: 1877-1884 (2002). | PubMed |
Filippin, L., Abad, M. F. C., Gastaldello, S., Magalhăes, P. J., Sandonŕ, D., and Pozzan, T., Improved strategies for the delivery of GFP-based calcium sensors into the mitochondrial matrix., Cell Calcium 37: 129-136 (2005). | PubMed |
Finley, K. R., Davidson, A. E., and Ekker, S. C., Three-color imaging using fluorescent proteins in living Zebrafish embryos., BioTechniques 31: 66-72 (2001). | PubMed |
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Fischer, M., Haase, I., Simmeth, E., Gerisch, G., and Müller-Taubenberger, A., A brilliant monomeric red fluorescent protein to visualize cytoskeleton dynamics in Dictyostelium., FEBS Letters 577: 227-232 (2004). | PubMed |
Follenius-Wund, A., Bourotte, M., Schmitt, M., Lyice, F., Lami, H., Bourguignon, J.-J., and Pigault, C., Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process., Biophysical Journal 85: 1839-1850 (2003). | PubMed |
Fradkov, A. F., Chen, Y., Ding, L., Barsova, E. V., Matz, M. V., and Lukyanov, S. A., Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence., FEBS Letters 479: 127-130 (2000). | PubMed |
Fradkov, A. F., Verkhusha, V. V., Staroverov, D. B., Bulina, M. E., Yanushevich, Y. G., Martynov, V. I., Lukyanov, S., and Lukyanov, K. A., Far-red fluorescent tag for protein labelling., Biochemical Journal 368: 17-21 (2002). | PubMed |
Gaietta, G., Deerinck, T. J., Adams, S. R., Bouwer, J., Tour, O., Laird, D. W., Sosinsky, G. E., Tsien, R. Y., and Ellisman, M. H., Multicolor and electron microscopic imaging of connexin trafficking., Science 296: 503-507 (2002). | PubMed |
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Griesbeck, O., Baird, G. S., Campbell, R. E., Zacharias, D. A., and Tsien, R. Y., Reducing the environmental sensitivity of yellow fluorescent protein., Journal of Biological Chemistry 276: 29188-29194 (2001). | PubMed |
Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K., and Tsien, R. Y., The structure of the chromophore within DsRed, a red fluorescent protein from coral., Proceedings of the National Academy of Sciences (USA) 97: 11990-11995 (2000). | PubMed |
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Gurskaya, N. G., Fradkov, A. F., Pounkova, N. I., Staroverov, D. B., Bulina, M. E., Yanushevich, Y. G., Labas, Y. A., Lukyanov, S., and Lukyanov, K. A., A colourless green fluorescent protein homologue from the non-fluorescent hydromedusa Aequorea coerulescens and its fluorescent mutants., Biochemical Journal 373: 403-408 (2003). | PubMed |
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| PubMed |
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| PubMed |
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