Strengths and weaknesses of recently engineered red fluorescent proteins evaluated in live cells using fluorescence correlation spectroscopy

International Journal of Molecular Sciences

Volumn 14, Issue 10, 2013, Pages 20340-20358

  Siegel, Amanda P ^a   Baird, Michelle A ^b   Davidson, Michael W ^b   Day, Richard N ^a  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Diffusion; Flickering; Fluorescent correlation spectroscopy (FCS); Fluorescent protein; Intrinsic brightness

Indexed keywords

CCAAT ENHANCER BINDING PROTEIN ALPHA; HYBRID PROTEIN; LEUCINE ZIPPER PROTEIN; RED FLUORESCENT PROTEIN;

ACCURACY; ANIMAL CELL; ARTICLE; BIOENGINEERING; CELL STRAIN; CELL STRAIN GHFT1; CONTROLLED STUDY; DIFFUSION; FLUORESCENCE ANALYSIS; FLUORESCENCE CORRELATION SPECTROSCOPY; MICROSCOPY; MOLECULAR BIOLOGY; MOUSE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STABILITY;

ANIMALS; CELL LINE; FLUORESCENCE; LUMINESCENT PROTEINS; MICE; SPECTROMETRY, FLUORESCENCE;

EID: 84885906578     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms141020340     Document Type: Article

References (27)

1. Day, R.N.; Davidson, M.W. The fluorescent protein palette: Tools for cellular imaging. Chem. Soc. Rev. 2009, 38, 2887-2921.
2. Matz, M.V.; Fradkov, A.F.; Labas, Y.A.; Savitsky, A.P.; Zaraisky, A.G.; Markelov, M.L.; Lukyanov, S.A. Fluorescent proteins from nonbioluminescent Anthozoa species. Nat. Biotech. 1999, 17, 969-973.
3. Shaner, N.C.; Campbell, R.E.; Steinbach, P.A.; Giepmans, B.N.; Palmer, A.E.; Tsien, R.Y. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 2004, 22, 1567-1572.
4. Shaner, N.C.; Steinbach, P.A.; Tsien, R.Y. A guide to choosing fluorescent proteins. Nat. Meth. 2005, 2, 905-909.
5. Hendrix, J.; Flors, C.; Dedecker, P.; Hofkens, J.; Engelborghs, Y. Dark states in monomeric red fluorescent proteins studied by fluorescence correlation and single molecule spectroscopy. Biophys. J. 2008, 94, 4103-4113.
6. Shu, X.; Shaner, N.C.; Yarbrough, C.A.; Tsien, R.Y.; Remington, S.J. Novel chromophores and buried charges control color in mFruits. Biochemistry 2006, 45, 9639-9647.
7. Subach, O.M.; Malashkevich, V.N.; Zencheck, W.D.; Morozova, K.S.; Piatkevich, K.D.; Almo, S.C.; Verkhusha, V.V. Structural characterization of acylimine-containing blue and red chromophores in mTagBFP and TagRFP fluorescent proteins. Chem. Biol. 2010, 17, 333-341.
8. Shemiakina, I.; Ermakova, G.; Cranfill, P.; Baird, M.; Evans, R.; Souslova, E.; Staroverov, D.; Gorokhovatsky, A.; Putintseva, E.; Gorodnicheva, T. A monomeric red fluorescent protein with low cytotoxicity. Nat. Commun. 2012, 3, doi:10.1038/ncomms2208.
9. Lam, A.J.; St-Pierre, F.; Gong, Y.; Marshall, J.D.; Cranfill, P.J.; Baird, M.A.; McKeown, M.R.; Wiedenmann, J.; Davidson, M.W.; Schnitzer, M.J. Improving FRET dynamic range with bright green and red fluorescent proteins. Nat. Methods 2012, 9, 1005-1012.
10. Kredel, S.; Oswald, F.; Nienhaus, K.; Deuschle, K.; Röcker, C.; Wolff, M.; Heilker, R.; Nienhaus, G.U.; Wiedenmann, J. mRuby, a bright monomeric red fluorescent protein for labeling of subcellular structures. PLoS One 2009, 4, e4391.
11. Shaner, N.C.; Lin, M.Z.; McKeown, M.R.; Steinbach, P.A.; Hazelwood, K.L.; Davidson, M.W.; Tsien, R.Y. Improving the photostability of bright monomeric orange and red fluorescent proteins. Nat. Methods 2008, 5, 545-551.
12. 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. Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat. Methods 2007, 4, 555-557.
13. Dean, K.M.; Lubbeck, J.L.; Binder, J.K.; Schwall, L.R.; Jimenez, R.; Palmer, A.E. Analysis of red-fluorescent proteins provides insight into dark-state conversion and photodegradation. Biophys. J. 2011, 101, 961-969.
14. Siegel, A.P.; Hays, N.M.; Day, R.N. Unraveling transcription factor interactions with heterochromatin protein 1 using fluorescence lifetime imaging microscopy and fluorescence correlation spectroscopy. J. Biomed. Opt. 2013, 18, doi:10.1117/1.JBO.18.2.02500.
15. Schenk, A.; Ivanchenko, S.; Röcker, C.; Wiedenmann, J.; Nienhaus, G.U. Photodynamics of red fluorescent proteins studied by fluorescence correlation spectroscopy. Biophys. J. 2004, 86, 384-394.
16. Burnette, D.T.; Sengupta, P.; Dai, Y.; Lippincott-Schwartz, J.; Kachar, B. Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules. Proc. Natl. Acad. Sci. USA 2011, 108, 21081-21086.
17. Drobizhev, M.; Hughes, T.E.; Stepanenko, Y.; Wnuk, P.; O'Donnell, K.; Scott, J.N.; Callis, P.R.; Mikhaylov, A.; Dokken, L.; Rebane, A. Primary role of the chromophore bond length Alternation in reversible photoconversion of red fluorescence proteins. Sci. Rep. 2012, 2, doi:10.1038/srep00688.
18. Enderlein, J.; Gregor, I. Using fluorescence lifetime for discriminating detector afterpulsing in fluorescence-correlation spectroscopy. Rev. Sci. Instrum. 2005, 76, 033102:1-033102:5.
19. Markwardt, M.L.; Kremers, G.J.; Kraft, C.A.; Ray, K.; Cranfill, P.J.C.; Wilson, K.A.; Day, R.N.; Wachter, R.M.; Davidson, M.W.; Rizzo, M.A. An improved cerulean fluorescent protein with enhanced brightness and reduced reversible photoswitching. PLoS One 2011, 6, e17896.
20. Landschulz, W.H.; Johnson, P.F.; McKnight, S.L. The leucine zipper: A hypothetical structure common to a new class of DNA binding proteins. Science 1988, 240, 1759-1764.
21. Bancaud, A.; Huet, S.; Daigle, N.; Mozziconacci, J.; Beaudouin, J.; Ellenberg, J. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J. 2009, 28, 3785-3798.
22. Siegel, A.P.; Hays, N.M.; Day, R.N. Dynamic nuclear protein interactions investigated using fluorescence lifetime and fluorescence fluctuation spectroscopy. Proc. SPIE 2012, 8226, doi:10.1117/12.912883.
23. Wiedenmann, J.; Schenk, A.; Röcker, C.; Girod, A.; Spindler, K.-D.; Nienhaus, G.U. A far-red fluorescent protein with fast maturation and reduced oligomerization tendency from Entacmaea quadricolor (Anthozoa, Actinaria). Proc. Natl. Acad. Sci. USA 2002, 99, 11646-11651.
24. Subach, F.V.; Patterson, G.H.; Renz, M.; Lippincott-Schwartz, J.; Verkhusha, V.V. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells. J. Am. Chem. Soc. 2010, 132, 6481-6491.
25. Shaner, N.C.; Lambert, G.G.; Chammas, A.; Ni, Y.; Cranfill, P.J.; Baird, M.A.; Sell, B.R.; Allen, J.R.; Day, R.N.; Israelsson, M.; et al. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat. Meth. 2013, 10, 407-409.
26. Gebhardt, J.C.M.; Suter, D.M.; Roy, R.; Zhao, Z.W.; Chapman, A.R.; Basu, S.; Maniatis, T.; Xie, X.S. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 2013, 10, 421-426.
27. Hanson, C.A.; Drake, K.R.; Baird, M.A.; Han, B.; Kraft, L.J.; Davidson, M.W.; Kenworthy, A.K. Overexpression of caveolin-1 is sufficient to phenocopy the behavior of a disease-associated mutant. Traffic 2013, 14, 663-677.