Probing intranuclear environments at the single-molecule level

Biophysical Journal

Volumn 94, Issue 7, 2008, Pages 2847-2858

  Grünwald, David ^a   Martin, Robert M ^b   Buschmann, Volker ^b,c,f   Bazett Jones, David P ^d,e   Leonhardt, Heinrich ^c   Kubitscheck, Ulrich ^a   Cardoso, M Cristina ^b  

^a UNIVERSITY OF BONN   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^c UNIVERSITY OF MUNICH   (Germany)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

^e ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^f PICOQUANT GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

STREPTAVIDIN;

ACTIVE TRANSPORT; ANIMAL; ARTICLE; CELL LINE; CELL NUCLEUS; CYTOLOGY; FLUORESCENCE MICROSCOPY; GENETIC PROCEDURES; METABOLISM; METHODOLOGY; MOUSE; MYOBLAST; PHYSIOLOGY; ULTRASTRUCTURE;

ACTIVE TRANSPORT, CELL NUCLEUS; ANIMALS; CELL LINE; CELL NUCLEUS; MICE; MICROSCOPY, FLUORESCENCE; MOLECULAR PROBE TECHNIQUES; MYOBLASTS; STREPTAVIDIN;

EID: 41649095235     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115014     Document Type: Article

References (37)

1. Handwerger, K. E., and J. G. Gall. 2006. Subnuclear organelles: new insights into form and function. Trends Cell Biol. 16:19-26.
2. Spector, D. L. 2001. Nuclear domains. J. Cell Sci. 114:2891-2893.
3. Leonhardt, H., H. P. Rahn, and M. C. Cardoso. 1999. Functional links between nuclear structure, gene expression, DNA replication, and methylation. Crit. Rev. Eukaryot. Gene Expr. 9:345-351.
4. Lang, I., M. Scholz, and R. Peters. 1986. Molecular mobility and nucleocytoplasmic flux in hepatoma cells. J. Cell Biol. 102:1183-1190.
5. Seksek, O., J. Biwersi, and A. S. Verkman. 1997. Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus. J. Cell Biol. 138:131-142.
6. Verkman, A. S. 2002. Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem. Sci. 27:27-33.
7. Görisch, S. M., K. Richter, M. O. Scheuermann, H. Herrmann, and P. Lichter. 2003. Diffusion-limited compartmentalization of mammalian cell nuclei assessed by microinjected macromolecules. Exp. Cell Res. 289:282-294.
8. Görisch, S. M., M. Wachsmuth, K. F. Toth, P. Lichter, and K. Rippe. 2005. Histone acetylation increases chromatin accessibility. J. Cell Sci. 118:5825-5834.
9. Verschure, P. J., I. van der Kraan, E. M. Manders, D. Hoogstraten, A. B. Houtsmuller, and R. van Driel. 2003. Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep. 4:861-866.
10. Görisch, S. M., P. Lichter, and K. Rippe. 2005. Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments. Histochem. Cell Biol. 123:217-228.
11. + RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells. J. Cell Biol. 165:191-202.
12. Politz, J. C., R. A. Tuft, T. Pederson, and R. H. Singer. 1999. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr. Biol. 9:285-291.
13. Politz, J. C., R. A. Tuft, K. V. Prasanth, N. Baudendistel, K. E. Fogarty, L. M. Lifshitz, J. Langowski, D. L. Spector, and T. Pederson. 2006. Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasm. Mol. Biol. Cell. 17:1239-1249.
14. Shav-Tal, Y., X. Darzacq, S. M. Shenoy, D. Fusco, S. M. Janicki, D. L. Spector, and R. H. Singer. 2004. Dynamics of single mRNPs in nuclei of living cells. Science. 304:1797-1800.
15. Vargas, D. Y., A. Raj, S. A. Marras, F. R. Kramer, and S. Tyagi. 2005. Mechanism of mRNA transport in the nucleus. Proc. Natl. Acad. Sci. USA. 102:17008-17013.
16. Gorski, S. A., M. Dundr, and T. Misteli. 2006. The road much traveled: trafficking in the cell nucleus. Curr. Opin. Cell Biol. 18:284-290.
17. Beaudouin, J., F. Mora-Bermudez, T. Klee, N. Daigle, and J. Ellenberg. 2006. Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys. J. 90:1878-1894.
18. Braga, J., J. M. Desterro, and M. Carmo-Fonseca. 2004. Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol. Biol. Cell. 15:4749-4760.
19. Cardoso, M. C., H. Leonhardt, and B. Nadal-Ginard. 1993. Reversal of terminal differentiation and control of DNA replication: cyclin A and Cdk2 specifically localize at subnuclear sites of DNA replication. Cell. 74:979-992.
20. Cardoso, M. C., C. Joseph, H. P. Rahn, R. Reusch, B. Nadal-Ginard, and H. Leonhardt. 1997. Mapping and use of a sequence that targets DNA ligase I to sites of DNA replication in vivo. J. Cell Biol. 139:579-587.
21. Sleeman, J., C. E. Lyon, M. Platani, J. P. Kreivi, and A. I. Lamond. 1998. Dynamic interactions between splicing snRNPs, coiled bodies and nucleoli revealed using snRNP protein fusions to the green fluorescent protein. Exp. Cell Res. 243:290-304.
22. Brero, A., H. P. Easwaran, D. Nowak, I. Grunewald, T. Cremer, H. Leonhardt, and M. C. Cardoso. 2005. Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation. J. Cell Biol. 169:733-743.
23. Sporbert, A., P. Domaing, H. Leonhardt, and M. C. Cardoso. 2005. PCNA acts as a stationary loading platform for transiently interacting Okazaki fragment maturation proteins. Nucleic Acids Res. 33:3521-3528.
24. Kubitscheck, U., D. Grünwald, A. Hoekstra, D. Rohleder, T. Kues, J. P. Siebrasse, and R. Peters. 2005. Nuclear transport of single molecules: dwell times at the nuclear pore complex. J. Cell Biol. 168:233-243.
25. Siebrasse, J. P., D. Grünwald, and U. Kubitscheck. 2007. Single-molecule tracking in eukaryotic cell nuclei. Anal. Bioanal. Chem. 387:41-44.
26. Leonhardt, H., H. P. Rahn, P. Weinzierl, A. Sporbert, T. Cremer, D. Zink, and M. C. Cardoso. 2000. Dynamics of DNA replication factories in living cells. J. Cell Biol. 149:271-280.
27. Kues, T., A. Dickmanns, R. Lührmann, R. Peters, and U. Kubitscheck. 2001. High intranuclear mobility and dynamic clustering of the splicing factor U1 snRNP observed by single particle tracking. Proc. Natl. Acad. Sci. USA. 98:12021-12026.
28. Kues, T., and U. Kubitscheck. 2002. Single molecule motion perpendicular to the focal plane of a microscope: application to splicing factor dynamics within the cell nucleus. Single Mol. 3:218-224.
29. Saxton, M. J., and K. Jacobson. 1997. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26:373-399.
30. Crank, J. 1975. The Mathematics of Diffusion. Clarendon Press, Oxford.
31. Eskiw, C. H., G. Dellaire, J. S. Mymryk, and D. P. Bazett-Jones. 2003. Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly. J. Cell Sci. 116:4455-4466.
32. Dellaire, G., R. Nisman, and D. P. Bazett-Jones. 2004. Correlative light and electron spectroscopic imaging of chromatin in situ. Methods Enzymol. 375:456-478.
33. Kubitscheck, U., O. Kückmann, T. Kues, and R. Peters. 2000. Imaging and tracking of single GFP molecules in solution. Biophys. J. 78:2170-2179.
34. Grünwald, D., B. Spottke, V. Buschmann, and U. Kubitscheck. 2006. Intranuclear binding kinetics and mobility of single U1 snRNP particles in living cells. Mol. Biol. Cell. 17:5017-5027.
35. Grünwald, D., A. Hoekstra, T. Dange, V. Buschmann, and U. Kubitscheck. 2006. Direct observation of single protein molecules in aqueous solution. ChemPhysChem. 7:812-815.
36. Handwerger, K. E., J. A. Cordero, and J. G. Gall. 2005. Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. Mol. Biol. Cell. 16:202-211.
37. Weidemann, T., M. Wachsmuth, T. A. Knoch, G. Muller, W. Waldeck, and J. Langowski. 2003. Counting nucleosomes in living cells with a combination of fluorescence correlation spectroscopy and confocal imaging. J. Mol. Biol. 334:229-240.