Chapter 12 Reflections on FRET imaging. Formalism, probes, and implementation

Laboratory Techniques in Biochemistry and Molecular Biology

Volumn 33, Issue C, 2009, Pages 475-517

  Jares Erijman, Elizabeth A ^a   Jovin, Thomas M ^b  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 59249084438     PISSN: 00757535     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0075-7535(08)00012-0     Document Type: Review

References (149)

1. Jares-Erijman E.A., and Jovin T.M. FRET imaging. Nat. Biotechnol. 21 (2003) 1387-1395
2. Jares-Erijman E.A., and Jovin T.M. Imaging molecular interactions in living cells by FRET microscopy. Curr. Opin. Chem. Biol. 10 (2006) 409-416
3. van Manen H.J., Verkuijlen P., Wittendorp P., Subramaniam V., van den Berg T.K., Roos D., and Otto C. Refractive index sensing of green fluorescent proteins in living cells using fluorescence lifetime imaging microscopy. Biophys. J. 94 (2008) L67-L69
4. Beutler M., Makrogianneli K., Vermeij R.J., Keppler M., Ng T., Jovin T.M., and Heintzmann R. satFRET: Estimation of Förster resonance energy transfer by acceptor saturation. Eur. J. Biophys. (2008) DOI: 10.1007/s00249-008-0361-5
5. Heintzmann R., Jovin T.M., and Cremer C. Saturated patterned excitation microscopy-a novel concept for optical resolution improvement. J. Opt. Soc. Am. A 19 (2002) 1599-1609
6. Colyer R.A., Lee C., and Gratton E. A novel fluorescence lifetime imaging system that optimizes photon efficiency. Microsc. Res. Tech. 71 (2008) 201-213
7. Esposito A., Gerritsen H.C., Oggier T., Lustenberger F., and Wouters F.S. Innovating lifetime microscopy: A compact and simple tool for life sciences, screening, and diagnostics. J. Biomed. Opt. 11 (2006) 34016
8. Padilla-Parra S., Auduge N., Coppey-Moisan M., and Tramier M. Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells. Biophys. J (2008) DOI: 10.1529/biophysj.108.131276
9. Sanden T., Persson G., Thyberg P., Blom H., and Widengren J. Monitoring kinetics of highly environment sensitive states of fluorescent molecules by modulated excitation and time-averaged fluorescence intensity recording. Anal. Chem. 79 (2007) 3330-3341
10. Spriet C., Trinel D., Riquet F., Vandenbunder B., Usson Y., and Heliot L. Enhanced FRET contrast in lifetime imaging. Cytometry A 73A (2008) 745-753
11. Diaspro A.E. Special Issue: Advanced multiphoton and fluorescence lifetime imaging techniques. Microsc. Res. Tech. 70 (2007) 397-492
12. Rakich P., Dahlem M., Tandon S.N., Ibanescu M., Soljacic M., Petrich G.S., Joannopoulos J.D., Kolodziejski L.A., and Ippen E.P. Achieving centimetre-scale super-collimation in a large area 2D photonic crystal. Nat. Mater. 5 (2006) 93-96
13. Tada J., Kono T., Suda A., Mizuno H., Miyawaki A., Midorikawa K., and Kannari F. Adaptively controlled supercontinuum pulse from a microstructure fiber for two-photon excited fluorescence microscopy. Appl. Opt. 46 (2007) 3023-3030
14. MacKinnon N. Spectrally programmable light engine for in vitro or in vivo molecular imaging and spectroscopy. Appl. Opt. 44 (2005) 2033-2044
15. Forde T.S., and Hanley Q.S. Spectrally resolved frequency domain analysis of multi-fluorophore systems undergoing energy transfer. Appl. Spectrosc. 60 (2006) 1442-1452
16. Hanley Q.S., Murray P.I., and Forde T.S. Microspectroscopic fluorescence analysis with prism-based imaging spectrometers: Review and current studies. Cytometry A 69 (2006) 759-766
17. Ramanujan V.K., Biener-Ramanujan E., Armmer K., Centonze V.E., and Herman B.A. Spectral kinetics ratiometry: A simple approach for real-time monitoring of fluorophore distributions in living cells. Cytometry A 69 (2006) 912-919
18. Thaler C., and Vogel S.S. Quantitative linear unmixing of CFP and YFP from spectral images acquired with two-photon excitation. Cytometry A 69 (2006) 904-911
19. Wlodarczyk J., Woehler A., Kobe F., Ponimaskin E., Zeug A., and Neher E. Analysis of FRET-signals in the presence of free donors and acceptors. Biophys. J. 94 (2008) 986-1000
20. Zheng J. Spectroscopy-based quantitative fluorescence resonance energy transfer analysis. Methods Mol. Biol. 337 (2006) 65-77
21. Eggeling C., Widengren J., Brand L., Schaffer J., Felekyan S., and Seidel C.A. Analysis of photobleaching in single-molecule multicolor excitation and Forster resonance energy transfer measurements. J. Phys. Chem. A 110 (2006) 2979-2995
22. Kalinin S., Felekyan S., Antonik M., and Seidel C.A. Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer. J. Phys. Chem. B 111 (2007) 10253-10262
23. Lee N.K., Kapanidis A.N., Koh H.R., Korlann Y., Ho S.O., Kim Y., Gassman N., Kim S.K., and Weiss S. Three-color alternating-laser excitation of single molecules: Monitoring multiple interactions and distances. Biophys. J. 92 (2007) 303-312
24. Nir E., Michalet X., Hamadani K.M., Laurence T.A., Neuhauser D., Kovchegov Y., and Weiss S. Shot-noise limited single-molecule FRET histograms: Comparison between theory and experiments. J. Phys. Chem. B 110 (2006) 22103-22124
25. Rasnik I., McKinney S.A., and Ha T. Surfaces and orientations: Much to FRET about?. Acc. Chem. Res. 38 (2005) 542-548
26. Widengren J., Kudryavtsev V., Antonik M., Berger S., Gerken M., and Seidel C.A. Single-molecule detection and identification of multiple species by multiparameter fluorescence detection. Anal. Chem. 78 (2006) 2039-2050
27. Kong X., Nir E., Hamadani K., and Weiss S. Photobleaching pathways in single-molecule FRET experiments. J. Am. Chem. Soc. 129 (2007) 4643-4654
28. Widengren J., Chmyrov A., Eggeling C., Lofdahl P.A., and Seidel C.A. Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy. J. Phys. Chem. A 111 (2007) 429-440
29. Hoebe R.A., Van Oven C.H., Gadella Jr. T.W., Dhonukshe P.B., Van Noorden C.J., and Manders E.M. Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging. Nat. Biotechnol. 25 (2007) 249-253
30. Van Munster E.B., Kremers G.J., Adjobo-Hermans M.J., and Gadella Jr. T.W. Fluorescence resonance energy transfer (FRET) measurement by gradual acceptor photobleaching. J. Microsc. 218 (2005) 253-262
31. Coulon V., Audet M., Homburger V., Bockaert J., Fagni L., Bouvier M., and Perroy J. Subcellular imaging of dynamic protein interactions by bioluminescence resonance energy transfer. Biophys. J. 94 (2008) 1001-1009
32. Xu X., Soutto M., Xie Q., Servick S., Subramanian C., von Arnim A.G., and Johnson C.H. Imaging protein interactions with bioluminescence resonance energy transfer (BRET) in plant and mammalian cells and tissues. Proc. Natl. Acad. Sci. USA 104 (2007) 10264-10269
33. Mao S., Benninger R.K., Yan Y., Petchprayoon C., Jackson D., Easley C.J., Piston D.W., and Marriott G. Optical lock-in detection of FRET using synthetic and genetically encoded optical switches. Biophys. J. 94 (2008) 4515-4524
34. Santoso Y., Hwang L.C., Le Reste L., and Kapanidis A.N. Red light, green light: Probing single molecules using alternating-laser excitation. Biochem. Soc. Trans. 36 (2008) 738-744
35. Cohen-Kashi M., Namer Y., and Deutsch M. Fluorescence resonance energy transfer imaging via fluorescence polarization measurement. J. Biomed. Opt. 11 (2006) 34015
36. Fisz J.J. Another look at magic-angle-detected fluorescence and emission anisotropy decays in fluorescence microscopy. J. Phys. Chem. A 111 (2007) 12867-12870
37. Fisz J.J. Fluorescence polarization spectroscopy at combined high-aperture excitation and detection: Application to one-photon-excitation fluorescence microscopy. J. Phys. Chem. A 111 (2007) 8606-8621
38. Fixler D., Namer Y., Yishay Y., and Deutsch M. Influence of fluorescence anisotropy on fluorescence intensity and lifetime measurement: theory, simulations and experiments. IEEE Trans. Biomed. Eng. 53 (2006) 1141-1152
39. Rizzo M.A., and Piston D.W. High-contrast imaging of fluorescent protein FRET by fluorescence polarization microscopy. Biophys. J. 88 (2005) L14-L16
40. Chen H., Puhl III H.L., Koushik S.V., Vogel S.S., and Ikeda S.R. Measurement of FRET efficiency and ratio of donor to acceptor concentration in living cells. Biophys. J. 91 (2006) L39-L41
41. Domingo B., Sabariegos R., Picazo F., and Llopis J. Imaging FRET standards by steady-state fluorescence and lifetime methods. Microsc. Res. Tech. 70 (2007) 1010-1021
42. Schwartz J.W., Piston D., and DeFelice L.J. Molecular microfluorometry: Converting arbitrary fluorescence units into absolute molecular concentrations to study binding kinetics and stoichiometry in transporters. Handb. Exp. Pharmacol. (2006) 23-57
43. Vogel S.S., Thaler C., and Koushik S.V. Fanciful FRET. Sci STKE 2006 (2006) re2
44. Wallrabe H., Chen Y., Periasamy A., and Barroso M. Issues in confocal microscopy for quantitative FRET analysis. Microsc. Res. Tech. 69 (2006) 196-206
45. Nagy P., Vereb G., and Damjanovich S. Measuring FRET in flow cytometry and microscopy. Curr. Prot. Microsc. (2006) 12.18.11-12.18.13
46. Szöllösi J., Damjanovich S., Nagy P., Vereb G., and Mátyus L. Principles of resonance energy transfer. Curr. Prot. Cell Biol. (2006) 1.12.11-11.12.16
47. Rodighiero S., Bazzini C., Ritter M., Furst J., Botta G., Meyer G., and Paulmichl M. Fixation, mounting and sealing with nail polish of cell specimens lead to incorrect FRET measurements using acceptor photobleaching. Cell Physiol. Biochem. 21 (2008) 489-498
48. Hoppe A.D., Shorte S.L., Swanson J.A., and Heintzmann R. Three-dimensional FRET reconstruction microscopy for analysis of dynamic molecular interactions in live cells. Biophys. J. 95 (2008) 400-418
49. van Rheenen J., Langeslag M., and Jalink K. Correcting confocal acquisition to optimize imaging of fluorescence resonance energy transfer by sensitized emission. Biophys. J. 86 (2004) 2517-2529
50. Li E., Placone J., Merzlyakov M., and Hristova K. Quantitative measurements of protein interactions in a crowded cellular environment. Anal. Chem. 80 (2008) 5976-5985
51. Posokhov Y.O., Merzlyakov M., Hristova K., and Ladokhin A.S. A simple "proximity" correction for Forster resonance energy transfer efficiency determination in membranes using lifetime measurements. Anal. Biochem. 380 (2008) 134-136
52. Allen M.D., and Zhang J. A tunable FRET circuit for engineering fluorescent biosensors. Angew. Chem. Int. Ed. Engl. 47 (2008) 500-502
53. Fazekas Z., Petras M., Fabian A., Palyi-Krekk Z., Nagy P., Damjanovich S., Vereb G., and Szollosi J. Two-sided fluorescence resonance energy transfer for assessing molecular interactions of up to three distinct species in confocal microscopy. Cytometry A 73 (2008) 209-219
54. Piljic A., and Schultz C. Simultaneous recording of multiple cellular events by FRET. ACS Chem. Biol. 3 (2008) 156-160
55. Kudryavtsev V., Felekyan S., Wozniak A.K., Konig M., Sandhagen C., Kuhnemuth R., Seidel C.A., and Oesterhelt F. Monitoring dynamic systems with multiparameter fluorescence imaging. Anal. Bioanal. Chem. 387 (2007) 71-82
56. Heintzmann R., and Ficz G. Breaking the resolution limit in light microscopy. Briefings Funct. Genom. Proteom. 5 (2007) 289-301
57. Bates M., Huang B., Dempsey G.T., and Zhuang X. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317 (2007) 1749-1753
58. Hell S.W. Far-field optical nanoscopy. Science 316 (2007) 1153-1158
59. Hess S.T., Girirajan T.P.K., and Mason M.S. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91 (2006) 4258-4272
60. Marushchak D., and Johansson L.B. On the quantitative treatment of donor-donor energy migration in regularly aggregated proteins. J. Fluoresc. 15 (2005) 797-803
61. Tramier M., and Coppey-Moisan M. Fluorescence anisotropy imaging microscopy for homo-FRET in living cells. Methods Cell Biol. 85 (2008) 395-414
62. Yeow E.K.L., and Clayton A.H.A. Enumeration of oligomerization states of membrane proteins in living cells by homo-FRET spectroscopy and microscopy: Theory and application. Biophys. J. 92 (2007) 3098-3104
63. Szent-Gyorgyi C., Schmidt B.F., Creeger Y., Fisher G.W., Zakel K.L., Adler S., Fitzpatrick J.A., Woolford C.A., Yan Q., Vasilev K.V., Berget P., Bruchez M., et al. Fluorogen activating proteins: Technology for imaging and assaying cell surface proteins. Nat. Biotechnol. 26 (2007) 235-240
64. Szabó A., Horváth G., Szöllösi J., and Nagy P. Quantitative characterization of the large-scale association of ErbB1 and ErbB2 by flow cytometric homo-FRET measurements. Biophys. J. 95 (2008) 2086-2096
65. Demchenko A.P. Optimization of fluorescence response in the design of molecular biosensors. Anal. Biochem. 343 (2005) 1-22
66. O'Hare H.M., Johnsson K., and Gautier A. Chemical probes shed light on protein function. Curr. Opin. Struct. Biol. 17 (2007) 488-494
67. Sapsford K.E., Berti L., and Medintz I.L. Materials for fluorescence resonance energy transfer analysis: Beyond traditional donor-acceptor combinations. Angew. Chem. Int. Ed. Engl. 45 (2006) 4562-4589
68. Waggoner A. Fluorescent labels for proteomics and genomics. Curr. Opin. Chem. Biol. 10 (2006) 62-66
69. Bakalova R., Zhelev Z., Aoki I., and Kanno I. Designing quantum dot probes. Nat. Photonics 1 (2007) 487-489
70. Chen I., Choi Y.A., and Ting A.Y. Phage display evolution of a peptide substrate for yeast biotin ligase and application to two-color quantum dot labeling of cell surface proteins. J. Am. Chem. Soc. 129 (2007) 6619-6625
71. Clarke S.J., Hollmann C.A., Aldaye F.A., and Nadeau J.L. Effect of ligand density on the spectral, physical, and biological characteristics of CdSe/ZnS quantum dots. Bioconjug. Chem. 19 (2008) 562-568
72. Giepmans B.N., Adams S.R., Ellisman M.H., and Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 312 (2006) 217-224
73. Howarth M., Takao K., Hayashi Y., and Ting A.Y. Targeting quantum dots to surface proteins in living cells with biotin ligase. Proc. Natl. Acad. Sci. USA 102 (2005) 7583-7588
74. Landegren U., Schallmeiner E., Nilsson M., Fredriksson S., Baner J., Gullberg M., Jarvius J., Gustafsdottir S., Dahl F., Soderberg O., et al. Molecular tools for a molecular medicine: Analyzing genes, transcripts and proteins using padlock and proximity probes. J. Mol. Recog. 17 (2004) 194-197
75. Pinaud F., Michalet X., Bentolila L.A., Tsay J.M., Doose S., Li J.J., Iyer G., and Weiss S. Advances in fluorescence imaging with quantum dot bio-probes. Biomaterials 27 (2006) 1679-1687
76. Smith A.M., Ruan G., Rhyner M.N., and Nie S. Engineering luminescent quantum dots for in vivo molecular and cellular Imaging. Ann. Biomed. Eng. 34 (2006) 3-14
77. Zhang Y., So M.-K., Loening A.M., Yao H., Gambhir S.S., and Rao J. HaloTag protein-mediated site-specific conjugation of bioluminescent proteins to quantum dots. Angew. Chem. Int. Ed. Engl. 45 (2006) 4936-4940
78. Borisov S.M., Mayr T., Karasyov A.A., Klimant I., Chojnacki P., Moser C., Nagl S., Schaeferling M., Stich M.I., Vasylevska G.S., et al. New plastic microparticles and nanoparticles for fluorescence sensing and encoding. In: Berberan M.N. (Ed). Fluorescence of Supermolecules, Polymers, and Nanosystems (2007), Springer, Berlin 431-463
79. Pregibon D.C., Toner M., and Doyle P.S. Multifunctional encoded particles for high-throughput biomolecule analysis. Science 315 (2007) 1393-1396
80. Qin L., Banholzer M.J., Millstone J.E., and Mirkin C.A. Nanodisk codes. Nano Lett. 7 (2007) 3849-3852
81. Seferos D.S., Giljohann D.A., Hill H.D., Prigodich A.E., and Mirkin C.A. Nano-flares: Probes for transfection and mRNA detection in living cells. J. Am. Chem. Soc. 129 (2007) 15477-15479
82. Tyner K.M., Kopelman R., and Philbert M.A. "Nanosized voltmeter" enables cellular-wide electric field mapping. Biophys. J. 93 (2007) 1163-1174
83. Burns A., Ow H., and Wiesner U. Fluorescent core-shell silica nanoparticles: Towards "Lab on a Particle" architectures for nanobiotechnology. Chem. Soc. Rev. 35 (2006) 1028-1042
84. Sukhanova A., and Nabiev I. Fluorescent nanocrystal-encoded microbeads for multiplexed cancer imaging and diagnosis. Crit. Rev. Oncol. Hematol (2008) DOI: 10.1016/j.critrevonc.2008.05.006
85. Zhang B., Cheng J., Gong X., Dong X., Liu X., Ma G., and Chang J. Facile fabrication of multi-colors high fluorescent/superparamagnetic nanoparticles. J. Colloid Interface Sci. 322 (2008) 485-490
86. Johnsson N., and Johnsson K. Chemical tools for biomolecular imaging. ACS Chem. Biol. 2 (2007) 31-38
87. Loudet A., and Burgues S.K. BODIPY dyes and their derivatives: Syntheses and spectroscopic properties. Chem. Rev. 107 (2007) 4891-4932
88. Miyawaki A., and Karasawa S. Memorizing spatiotemporal patterns. Nat. Chem. Biol. 3 (2007) 598-601
89. Piston D.W., and Kremers G.-J. Fluorescent protein FRET: The good, the bad and the ugly. Trends Biochem. Sci. 32 (2007) 407-414
90. Ai H.W., Shaner N.C., Cheng Z., Tsien R.Y., and Campbell R.E. Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins. Biochemistry 46 (2007) 5904-5910
91. Kremers G.J., Goedhart J., van den Heuvel D.J., Gerritsen H.C., and Gadella Jr. T.W. Improved green and blue fluorescent proteins for expression in bacteria and mammalian cells. Biochemistry 46 (2007) 3775-3783
92. Merzlyak E.M., Goedhart J., Shcherbo D., Bulina M.E., Shcheglov A.S., Fradkov A.F., Gaintzeva A., Lukyanov K.A., Lukyanov S., Gadella T.W., et al. Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat. Methods 4 (2007) 555-557
93. Olenych S.G., Claxton N.S., Ottenberg G.K., and Davidson M.W. The fluorescent protein color palette. Curr. Protoc Cell Biol. (2007) Chapter 21: Unit 21.5
94. Shaner N.C., Patterson G.H., and Davidson M.W. Advances in fluorescent protein technology. J. Cell Sci. 120 (2007) 4247-4260
95. Shimozono S., and Miyawaki A. Engineering FRET constructs using CFP and YFP. Methods Cell Biol. 85 (2008) 381-393
96. Tsutsui H., Karasawa S., Okamura Y., and Miyawaki A. Improving membrane voltage measurements using FRET with new fluorescent proteins. Nat. Methods 5 (2008) 683-685
97. van der Krogt G.N., Ogink J., Ponsioen B., and Jalink K. A comparison of donor-acceptor pairs for genetically encoded FRET sensors: Application to the Epac cAMP sensor as an example. PLoS ONE 3 (2008) e1916
98. Ganesan S., Ameer-Beg S.M., Ng T.T., Vojnovic B., and Wouters F.S. A dark yellow fluorescent protein (YFP)-based resonance energy-accepting chromoprotein (REACh) for Forster resonance energy transfer with GFP. Proc. Natl. Acad. Sci. USA 103 (2006) 4089-4094
99. Sakaue-Sawano A., Kurokawa H., Morimura T., Hanyu A., Hama H., Osawa H., Kashiwagi S., Fukami K., Miyata T., Miyoshi H., et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132 (2008) 487-498
100. Budzikiewicz H., Schafer M., Fernandez D.U., Matthijs S., and Cornelis P. Characterization of the chromophores of pyoverdins and related siderophores by electrospray tandem mass spectrometry. Biometals 20 (2007) 135-444
101. Bonasio R., Carman C.V., Kim E., Sage P.T., Love K.R., Mempel T.R., Springer T.A., and von Andrian U.H. Specific and covalent labeling of a membrane protein with organic fluorochromes and quantum dots. Proc. Natl. Acad. Sci. USA 104 (2007) 14753-14758
102. Smith J.J., Conrad D.W., Cuneo M.J., and Hellinga H.W. Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms. Protein Sci. 14 (2005) 64-73
103. Butlin N.G., and Meares C.F. Antibodies with infinite affinity: Origins and applications. Acc. Chem. Res. 39 (2006) 780-787
104. Carrico I.S., Carlson B.I., and Bertozzi C.R. Introducing genetically encoded aldehydes into proteins. Nat. Chem. Biol. 3 (2007) 321-322
105. Nonaka H., Tsukiji S., Ojida A., and Hamachi I. Non-enzymatic covalent protein labeling using a reactive tag. J. Am. Chem. Soc. 129 (2007) 15777-15779
106. Popp M.W., Antos J.M., Grotenbreg G.M., Spooner E., and Ploegh H.L. Sortagging: A versatile method for protein labeling. Nat. Chem. Biol. 3 (2007) 707-708
107. Tanaka T., Yamamoto T., Tsukiji S., and Nagamune T. Site-specific protein modification on living cells catalyzed by sortase. Chembiochem 9 (2008) 802-807
108. Busch G.K., Tate E.W., Gaffney P.R., Rosivatz E., Woscholski R., and Leatherbarrow R.J. Specific N-terminal protein labelling: Use of FMDV 3C protease and native chemical ligation. Chem. Commun. (2008) 3369-3371
109. Chattopadhaya S., Abu Bakar F.B., Srinivasan R., and Yao S.Q. In vivo imaging of a bacterial cell division protein using a protease-assisted small-molecule labeling approach. Chembiochem 9 (2008) 677-680
110. Kobayashi T., Shiratori M., Nakano H., Eguchi C., Shirai M., Naka D., and Shibui T. Short peptide tags increase the yield of C-terminally labeled protein. Biotechnol. Lett. 29 (2007) 1065-1073
111. Baskin J.M., Prescher J.A., Laughlin S.T., Agard N.J., Chang P.V., Miller I.A., Lo A., Codelli J.A., and Bertozzi C.R. Copper-free click chemistry for dynamic in vivo imaging. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 16793-16797
112. Blum G., von Degenfeld G., Merchant M.J., Blau H.M., and Bogyo M. Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. Nat. Chem. Biol. 3 (2007) 668-677
113. Bhunia A.K., and Miller S.C. Labeling tetracysteine-tagged proteins with a SplAsH of color: A modular approach to bis-arsenical fluorophores. Chembiochem 8 (2007) 1642-1645
114. Soh N. Selective chemical labeling of proteins with small fluorescent molecules based on metal-chelation methodology. Sensors 8 (2008) 1004-1024
115. Cao H., Chen B., Squier T.C., and Uljana Mayer M.U. CrAsH: A biarsenical multi-use affinity probe with low non-specific fluorescence. Chem. Comm. (2006) 2601-2603
116. Cao H., Xiong Y., Wang T., Chen B., Squier T.C., and Mayer M.U. A red Cy3-based biarsenical fluorescent probe targeted to a complementary binding peptide. J. Am. Chem. Soc. 129 (2007) 8672-8673
117. Luedtke N.W., Dexter R.J., Fried D.B., and Schepartz A. Surveying polypeptide and protein domain conformation and association with FlAsH and ReAsH. Nat. Chem. Biol. 3 (2007) 779-784
118. Liu B., Archer C.T., Burdine L., Gillette T.G., and Kodadek T. Label transfer chemistry for the characterization of protein-protein interactions. J. Am. Chem. Soc. 129 (2007) 12348-12349
119. Hearps A.C., Pryor M.J., Kuusisto H.V., Rawlinson S.M., Piller S.C., and Jan D.A. The biarsenical dye lumiotrade exhibits a reduced ability to specifically detect tetracysteine-containing proteins within live cells. J. Fluor. 17 (2007) 593-597
120. Spagnuolo C.C., Vermeij R.J., and Jares-Erijman E.A. Improved photostable FRET-competent biarsenical-tetracysteine probes based on fluorinated flluoresceins. J. Am. Chem. Soc. 128 (2006) 12040-13041
121. 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. Nat. Methods 4 (2007) 345-351
122. Maurel D., Comps-Agrar L., Brock C., Rives M.L., Bourrier E., Ayoub M.A., Bazin H., Tinel N., Durroux T., Prezeau L., et al. Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: Application to GPCR oligomerization. Nat. Methods 5 (2008) 561-567
123. 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 Chem. Biol. 2 (2007) 337-346
124. Wolfbeis O.S. The click reaction in the luminescent probing of metal ions, and its implications on biolabeling techniques. Angew. Chem. Int. Ed. Engl. 46 (2007) 2980-2982
125. Hohng S., and Ha T. Single-molecule quantum-dot fluorescence resonance energy transfer. Chemphyschem 6 (2005) 956-960
126. Roy R., Hohng S., and Ha T. A practical guide to single-molecule FRET. Nat. Methods 5 (2008) 507-516
127. Lidke D.S., Lidke K.A., Rieger B., Jovin T.M., and Arndt-Jovin D.J. Reaching out for signals: Filopodia sense EGF and respond by directed retrograde transport of activated receptors. J. Cell Biol. 170 (2005) 619-626
128. Susumu K., Uyeda H.T., Medintz I.L., Pons T., Delehanty J.B., and Mattoussi H. Enhancing the stability and biological functionalities of quantum dots via compact multifunctional ligands. J. Am. Chem. Soc. 129 (2007) 13988-13996
129. Dennis A.M., and Bao G. Quantum dot-fluorescent protein pairs as novel fluorescence resonance energy transfer probes. Nano Lett. 8 (2008) 1439-1445
130. Hering V.R., Gibson G., Schumacher R.I., Faljoni-Alario A., and Politi M.J. Energy transfer between CdSe/ZnS core/shell quantum dots and fluorescent proteins. Bioconjug. Chem. 18 (2007) 1705-1708
131. McGrath N., and Barroso M. Quantum dots as fluorescence resonance energy transfer donors in cells. J. Biomed. Opt. 13 (2008) 031210/1-031210/9
132. Baer R., and Rabani E. Theory of resonance energy transfer involving nanocrystals: The role of high multipoles. J. Chem. Phys. 128 (2008) 184710
133. Roberti M.J., Morgan M., Pietrasanta L., Jovin T.M., and Jares-Erijman E.A. Quantum dots as efficient triggers-sensors of α-synuclein amyloid aggregation in living cells. submitted (2008)
134. Giordano L., Jovin T.M., Irie M., and Jares-Erijman E.A. Diheteroarylethenes as thermally stable photoswitchable acceptors in photochromic fluorescence resonance energy transfer (pcFRET). J. Am. Chem. Soc. 124 (2002) 7481-7489
135. Fölling J., Polyakova S., Belov V., van Blaaderen A., Bossi M.L., and Hell S.W. Synthesis and characterization of photoswitchable fluorescent silica nanoparticles. Small 4 (2008) 134-142
136. Sakata T., Jackson D.K., Mao S., and Marriott G. Optically switchable chelates: Optical control and sensing of metal ions. J. Org. Chem. 73 (2008) 227-233
137. Soh N., Yoshida K., Nakajima H., Nakano K., Imato T., Fukaminato T., and Irie M. A fluorescent photochromic compound for labeling biomolecules. Chem. Commun. (2007) 5206-5208
138. Dedecker P., Hotta J.-I., Flors C., Sliwa M., Uji I.H., Roeffaers M.B.J., Ando R., Mizuno H., Miyawaki A., and Hofkens J. Subdiffraction imaging through the selective donut-mode depletion of thermally stable photoswitchable fluorophores: Numerical analysis and application to the fluorescent protein Dronpa. J. Am. Chem. Soc. 129 (2007) 16132-16141
139. Miskoski S., Giordano L., Etchehon M.H., Menendez G., Lidke K.A., Hagen G.M., Jovin T.M., and Jares-Erijman E.A. Spectroscopic modulation of multifunctionalized quantum dots for use as biological probes and effectors. Proc SPIE 6096 (2006) 60960X60961-60967
140. Jiao G., Thoresen L., Kim T., Haaland W., Gao F., Topp M., Hochstrasser R., Metzker M., and Burgess K. Syntheses, photophysical properties, and application of through-bond energy-transfer cassettes for biotechnology. Chemistry 12 (2006) 7816-7826
141. Li Y., Zhou X., and Ye D. Molecular beacons: An optimal multifunctional biological probe. Biochem. Biophys. Res. Commun. 373 (2008) 457-461
142. Shlyahovsky B., Weizmann Y., Nowarski R., Kotler M., and Willner I. Spotlighting of cocaine by autonomous aptamer-based machine. J. Am. Chem. Soc. 129 (2006) 3814-3815
143. Ellis-Davies G.C. Caged compounds: Photorelease technology for control of cellular chemistry and physiology. Nat. Methods 4 (2007) 619-628
144. Zheng G., Guo Y.M., and Li W.H. Photoactivatable and water soluble FRET dyes with high uncaging cross section. J. Am. Chem. Soc. 129 (2007) 10616-10617
145. Skirtach A.G., and Kreft O. Stimuli-sensitive nanotechnology for drug delivery. In: de Villiers M.M., Aramwit P., and Kwon G.S. (Eds). Nanotechnology in Drug Delivery (2007), Springer, Berlin 117-130
146. Hoffman A.S., and Stayton P.S. Conjugates of stimuli-responsive polymers and proteins. Prog. Polymer Sci. 32 (2007) 922-932
147. Pelah A., and Jovin T.M. Polymeric actuators for biological aapplications. Chemphyschem 8 (2007) 1757-1760
148. Protasenko V., Hull K.L., and Kuno M. Demonstration of a low-cost, single-molecule capable, multimode optical microscope. Chem. Educator 10 (2005) 269-282
149. Hagen G., Lidke K., Rieger B., Caarls W., Arndt-Jovin D., and Jovin T. Dynamics of membrane receptors: Single molecule tracking of quantum dot liganded epidermal growth factor. In: Ishii Y., and Yanagida T. (Eds). Single Molecule Dynamics (2007), Wiley, Orlando