Analysis of binding reactions by fluorescence recovery after photobleaching

Biophysical Journal

Volumn 86, Issue 6, 2004, Pages 3473-3495

  Sprague, Brian L ^a   Pego, Robert L ^b   Stavreva, Diana A ^a   McNally, James G ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOCORTICOID RECEPTOR; TRANSCRIPTION FACTOR;

ARTICLE; BINDING AFFINITY; CELL NUCLEUS MATRIX; DIFFUSION; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; MATHEMATICAL ANALYSIS; SOLUTION AND SOLUBILITY;

EID: 2942690158     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.026765     Document Type: Article

References (49)

1. Abramowitz, M., and I. A. Stegun. 1972. Bessel functions of integer order. In Handbook of Mathematical Functions. Dover Publications, New York. 377.
2. Arrio-Dupont, M., G. Foucault, M. Vacher, P. F. Devaux, and S. Cribier. 2000. Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells. Biophys. J. 78:901-907.
3. Axelrod, D., D. E. Koppel, J. Schlessinger, E. Elson, and W. W. Webb. 1976. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys. J. 16:1055-1069.
4. Berg, O. G. 1986. Effective diffusion rate through a polymer network: influence of nonspecific binding and intersegment transfer. Biopolymers. 25:811-821.
5. Berk, D. A., F. Yuan, M. Leunig, and R. K. Jain. 1997. Direct in vivo measurement of targeted binding in a human tumor xenograft. Proc. Natl. Acad. Sci. USA. 94:1785-1790.
6. Bulinski, J. C., D. J. Odde, B. J. Howell, E. D. Salmon, and C. M. Waterman-Storer. 2001. Rapid dynamics of the microtubule binding of ensconsin in vivo. J. Cell Sci. 114:3885-3897.
7. Carrero, G., D. McDonald, E. Crawford, G. de Vries, and M. J. Hendzel. 2003. Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins. Methods. 29:14-28.
8. Carslaw, H. S., and J. C. Jaeger. 1959. The Laplace transformation: problems on the cylinder and sphere. Composite cylindrical regions. In Conduction of Heat in Solids. Oxford University Press, New York. 345-347.
9. Coscoy, S., F. Waharte, A. Gautreau, M. Martin, D. Louvard, P. Mangeat, M. Arpin, and F. Amblard. 2002. Molecular analysis of microscopic ezrin dynamics by two-photon FRAP. Proc. Natl. Acad. Sci. USA. 99:12813-12818.
10. Crank, J. 1975. Diffusion and chemical reaction. In The Mathematics of Diffusion. Oxford University Press, New York. 326-351.
11. Deroo, B. J., C. Rentsch, S. Sampath, J. Young, D. B. DeFranco, and T. K. Archer. 2002. Proteasomal inhibition enhances glucocorticoid receptor transactivation and alters its subnuclear trafficking. Mol. Cell. Biol. 22:4113-4123.
12. Dou, Y., J. Bowen, Y. Liu, and M. A. Gorovsky. 2002. Phosphorylation and an ATP-dependent process increase the dynamic exchange of H1 in chromatin. J. Cell Biol. 158:1161-1170.
13. Dundr, M., U. Hoffmann-Rohrer, Q. Hu, I. Grummt, L. I. Rothblum, R. D. Phair, and T. Misteli. 2002. A kinetic framework for a mammalian RNA polymerase in vivo. Science. 298:1623-1626.
14. Edidin, M., Y. Zagyansky, and T. J. Lardner. 1976. Measurement of membrane protein lateral diffusion in single cells. Science. 191:466-468.
15. Elson, E. L. 1985. Fluorescence correlation spectroscopy and photobleaching recovery. Annu. Rev. Phys. Chem. 36:379-406.
16. Elson, E. L. 2001. Fluorescence correlation spectroscopy measures molecular transport in cells. Traffic. 2:789-796.
17. Elson, E. L., and D. Magde. 1974. Fluorescence correlation spectroscopy. I. Conceptual basis and theory. Biopolymers. 13:1-27.
18. Elson, E. L., and J. A. Reidler. 1979. Analysis of cell surface interactions by measurements of lateral mobility. J. Supramol. Struct. 12:481-489.
19. Feder, T. J., I. Brust-Mascher, J. P. Slattery, B. Baird, and W. W. Webb. 1996. Constrained diffusion or immobile fraction on cell surfaces: a new interpretation. Biophys. J. 70:2767-2773.
20. Fey, E. G., G. Krochmalnic, and S. Penman. 1986. The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy. J. Cell Biol. 102:1654-1665.
21. Hollenbeck, K. J. 1998. INVLAP.M: A MATLAB function for numerical inversion of Laplace transforms by the de Hoog algorithm. http://www.isva.dtu. dk/staff/karl/invlap.htm.
22. Houtsmuller, A. B., and W. Vermeulen. 2001. Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photobleaching. Histochem. Cell Biol. 115:13-21.
23. Icenogle, R. D., and E. Elson. 1983. Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. II. FPR and FCS measurements at low and high DNA concentrations. Biopolymers. 22:1949-1966.
24. Kaufman, E. N., and R. K. Jain. 1990. Quantification of transport and binding parameters using fluorescence recovery after photobleaching. Potential for in vivo applications. Biophys. J. 58:873-885.
25. Kaufman, E. N., and R. K. Jain. 1991. Measurement of mass transport and reaction parameters in bulk solution using photobleaching. Reaction limited binding regime. Biophys. J. 60:596-610.
26. Kimura, H., K. Sugaya, and P. R. Cook. 2002. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159:777-782.
27. Lieberman, B. A., and S. K. Nordeen. 1997. DNA intersegment transfer, how steroid receptors search for a target site. J. Biol. Chem. 272:1061-1068.
28. Liebman, P. A., and G. Entine. 1974. Lateral diffusion of visual pigment in photoreceptor disk membranes. Science. 185:457-459.
29. McNally, J. G., W. G. Muller, D. Walker, R. Wolford, and G. L. Hager. 2000. The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. Science. 287:1262-1265.
30. Meyvis, T. K., S. C. De Smedt, P. Van Oostveldt, and J. Demeester. 1999. Fluorescence recovery after photobleaching: a versatile tool for mobility and interaction measurements in pharmaceutical research. Pharm. Res. 16:1153-1162.
31. Misteli, T. 2001. Protein dynamics: implications for nuclear architecture and gene expression. Science. 291:843-847.
32. Müller, W. G., D. Walker, G. L. Hager, and J. G. McNally. 2001. Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J. Cell Biol. 154:33-48.
33. Pederson, T. 2000. Half a century of "the nuclear matrix." Mol. Biol. Cell. 11:799-805.
34. Phair, R. D., and T. Misteli. 2000. High mobility of proteins in the mammalian cell nucleus. Nature. 404:604-609.
35. Poo, M., and R. A. Cone. 1974. Lateral diffusion of rhodopsin in the photoreceptor membrane. Nature. 247:438-441.
36. Reits, E. A., and J. J. Neefjes. 2001. From fixed to FRAP: measuring protein mobility and activity in living cells. Nat. Cell Biol. 3: E145-E147.
37. Safranyos, R. G., S. Caveney, J. G. Miller, and N. O. Peterson. 1987. Relative roles of gap junction channels and cytoplasm in cell-to-cell diffusion of fluorescent tracers. Proc. Natl. Acad. Sci. USA. 84:2272-2276.
38. Schaaf, M. J. M., and J. A. Cidlowski. 2003. Molecular determinants of glucocorticoid receptor mobility in living cells: the importance of ligand affinity. Mol. Cell. Biol. 23:1922-1934.
39. Schlessinger, J., D. E. Koppel, D. Axelrod, K. Jacobson, W. W. Webb, and E. L. Elson. 1976. Lateral transport on cell membranes: mobility of concanavalin A receptors on myoblasts. Proc. Natl. Acad. Sci. USA. 73:2409-2413.
40. Siggia, E. D., J. Lippincott-Schwartz, and S. Bekiranov. 2000. Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery. Biophys. J. 79:1761-1770.
41. Soumpasis, D. M. 1983. Theoretical analysis of fluorescence photobleaching recovery experiments. Biophys. J. 41:95-97.
42. Stenoien, D. L., K. Patel, M. G. Mancini, M. Dutertre, C. L. Smith, B. W. O'Malley, and M. A. Mancini. 2001. FRAP reveals that mobility of oestrogen receptor-alpha is ligand- and proteasome-dependent. Nat. Cell Biol. 3:15-23.
43. Swaminathan, R., C. P. Hoang, and A. S. Verkman. 1997. Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophys. J. 72:1900-1907.
44. Tang, Y., and D. B. DeFranco. 1996. ATP-dependent release of glucocorticoid receptors from the nuclear matrix. Mol. Cell. Biol. 16:1989-2001.
45. Tardy, Y., J. L. McGrath, J. H. Hartwig, and C. F. Dewey. 1995. Interpreting photoactivated fluorescence microscopy measurements of steady-state actin dynamics. Biophys. J. 69:1674-1682.
46. Thompson, N. L., T. P. Burghardt, and D. Axelrod. 1981. Measuring surface dynamics of biomolecules by total internal reflection fluorescence with photobleaching recovery or correlation spectroscopy. Biophys. J. 33:435-454.
47. Walker, D., H. Htun, and G. L. Hager. 1999. Using inducible vectors to study intracellular trafficking of GFP-tagged steroid/nuclear receptors in living cells. Methods. 19:386-393.
48. Watson, G. N. 1944. A Treatise on the Theory of Bessel Functions. The MacMillan Company, New York.
49. White, J., and E. Stelzer. 1999. Photobleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol. 9:61-65.