The diffusion constant of a labeled protein sliding along DNA

European Physical Journal E

Volumn 34, Issue 3, 2011, Pages

  Bonnet, I ^a,b   Desbiolles, P ^a  

^a LABORATOIRE KASTLER BROSSEL   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BROWNIAN MOTION; DIFFUSION CONSTANT; DNA-PROTEIN INTERACTION; HOOKEAN SPRINGS; INDIVIDUAL PROTEINS; LABELED PROTEINS; LINEAR DIFFUSION; NANO-SIZED; PERIODIC POTENTIALS; PROTEIN DIFFUSION; QUANTUM DOT; RESTRICTION ENZYMES; SINGLE MOLECULE LEVEL;

BROWNIAN MOVEMENT; DIFFUSION; DNA; ENZYMES; FLUORESCENCE MICROSCOPY; FOKKER PLANCK EQUATION; IMAGING TECHNIQUES;

PROTEINS;

CARBOCYANINE; CYANINE DYE 3; DNA; FLUORESCENT DYE; GATATC SPECIFIC TYPE II DEOXYRIBONUCLEASES; GATATC-SPECIFIC TYPE II DEOXYRIBONUCLEASES; PROTEIN; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; DIFFUSION; METABOLISM; MOVEMENT (PHYSIOLOGY); STATISTICAL MODEL;

CARBOCYANINES; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIFFUSION; DNA; FLUORESCENT DYES; LINEAR MODELS; MODELS, BIOLOGICAL; MOVEMENT; PROTEINS;

EID: 79955832544     PISSN: 12928941     EISSN: 1292895X     Source Type: Journal    
DOI: 10.1140/epje/i2011-11025-8     Document Type: Article

References (38)

1. A.D. Riggs, S. Bourgeois, M. Cohn, J. Mol. Biol. 53, 401 (1970).
2. O.G. Berg, R.B. Winter, P.H. von Hippel, Biochemistry 20, 6929 (1981).
3. P.H. von Hippel, O.G. Berg, J. Biol. Chem. 264, 675 (1989).
4. S.E. Halford, J.F. Marko, Nucleic Acids Res. 32, 3040 (2004).
5. M. Coppey, O. Bénichou, R. Voituriez, M. Moreau, Biophys. J. 87, 1640 (2004).
6. H.-X. Zhou, Biophys. J. 88, 1608 (2005).
7. T. Hu, A.Y. Grosberg, B.I. Shklovskii, Biophys. J. 90, 2731 (2006).
8. B. van den Broek, M.A. Lomholt, S.M. Kalisch, R. Metzler, G.J. Wuite, Proc. Natl. Acad. Sci. U.S.A. 105, 15738 (2008).
9. M. Sheinman, Y. Kafri, Phys. Biol. 6, 016003 (2009).
10. C. Loverdo, O. Bénichou, R. Voituriez, A. Biebricher, I. Bonnet, P. Desbiolles, Phys. Rev. Lett. 102, 188101 (2009).
11. M. Díaz de la Rosa, E.F. Koslover, P.J. Mulligan, A.J. Spakowitz, Biophys. J. 98, 2943 (2010).
12. J. van Mameren, E.J. Peterman, G.J.Wuite, Nucleic Acids Res. 36, 4381 (2008).
13. J. Hilario, S.C. Kowalczykowski, Curr. Opin. Chem. Biol. 14, 15 (2010).
14. J. Gorman, E.C. Greene, Nat. Struct. Mol. Biol. 15, 768 (2008).
15. H. Kabata, O. Kurosawa, I. Arai, M. Washizu, S.A. Margarson, R.E. Glass, N. Shimamoto, Science 262, 1561 (1993).
16. A. Granéli, C.C. Yeykal, R.B. Robertson, E.C. Greene, Proc. Natl. Acad. Sci. U.S.A. 103, 1221 (2006).
17. P.C. Blainey, A.M. van Oijen, A. Banerjee, G.L. Verdine, X.S. Xie, Proc. Natl. Acad. Sci. U.S.A. 103, 5752 (2006).
18. Y.M. Wang, R.H. Austin, E.C. Cox, Phys. Rev. Lett. 97, 048302 (2006).
19. J.H. Kim, R.G. Larson, Nucleic Acids Res. 35, 3848 (2007).
20. J. Gorman, A. Chowdhury, J.A. Surtees, J. Shimada, D.R. Reichman, E. Alani, E.C. Greene, Mol. Cell 28, 359 (2007).
21. I. Bonnet, A. Biebricher, P.-L. Porté, C. Loverdo, O. Bénichou, R. Voituriez, C. Escudé, W.Wende, A. Pingoud, P. Desbiolles, Nucleic Acids Res. 36, 4118 (2008).
22. A. Tafvizi, F. Huang, J.S. Leith, A.R. Fersht, L.A. Mirny, A.M. van Oijen, Biophys. J. 95, L01 (2008).
23. N. Shimamoto, J. Biol. Chem. 274, 15293 (1999).
24. P.C. Blainey, G. Luo, S.C. Kou, W.F. Mangel, G.L. Verdine, B. Bagchi, X.S. Xie, Nat. Struct. Mol. Biol. 16, 1224 (2009).
25. N.M. Kad, H. Wang, G.G. Kennedy, D.M. Warshaw, B. van Houten, Mol. Cell 37, 702 (2010).
26. A. Biebricher, W. Wende, C. Escudé, A. Pingoud, P. Desbiolles, Biophys. J. 96, L50 (2009).
27. K.B. Zeldovich, J.-F. Joanny, J. Prost, Eur. Phys. J. E 17, 155 (2005).
28. M. Slutsky, L.A. Mirny, Biophys. J. 87, 4021 (2004).
29. N.S. Heyman, J.M. Burt, Biophys. J. 94, 840 (2008).
30. H. Risken, The Fokker-Planck Equation: Methods of Solutions and Applications, 3rd edition, Springer Series in Synergetics (Springer, 1996).
31. M. Dahan, S. Lévi, C. Luccardini, P. Rostaing, B. Riveau, A. Triller, Science 302, 442 (2003).
32. P. Fuchs, A. Parola, P.W. Robbins, E.R. Blout, Proc. Natl. Acad. Sci. U.S.A. 72, 3351 (1975).
33. Wolfram Research, Inc., Mathematica, Version 6.0 for Linux x86, Champaign, Illinois (2007).
34. J.M. Schurr, Biophys. Chem. 9, 413 (1979).
35. B. Bagchi, P.C. Blainey, X.S. Xie, J. Phys. Chem. B 112, 6282 (2008).
36. F.K. Winkler, A.E. Prota, in Restriction Endonucleases, Vol. 114, edited by A. Pingoud (Springer-Verlag, Berlin, Heidelberg, 2004).
37. A.B. Kochaniak, S. Habuchi, J.J. Loparo, D.J. Chang, K.A. Cimprich, J.C. Walter, A.M. van Oijen, J. Biol. Chem. 284, 17700 (2009).
38. A.G. Cherstvy, A.B. Kolomeisky, A.A. Kornyshev, J. Phys. Chem. B 112, 4741 (2008).