Nonspecific DNA-protein interaction: Why proteins can diffuse along DNA

Physical Review Letters

Volumn 102, Issue 22, 2009, Pages

  Dahirel, Vincent ^a   Paillusson, Fabien ^b   Jardat, Marie ^a   Barbi, Maria ^b   Victor, Jean Marc ^b  

^a SORBONNE UNIVERSITÉ   (France)

^b UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL CALCULATION; BOND INTERACTIONS; CONCAVE SHAPE; DNA-BINDING PROTEIN; DNA-PROTEIN INTERACTION; FINITE SURFACE; MONTE CARLO SIMULATION; NANO METER RANGE; PROTEIN CHARGE; SEQUENCE RECOGNITION; SINGLE MOLECULE EXPERIMENTS; SPECIFIC SITES; SURFACE SEPARATION; TARGET SEARCH;

DNA; FREE ENERGY; MONTE CARLO METHODS; MOSFET DEVICES; NUCLEIC ACIDS; PROTEINS; SUPRAMOLECULAR CHEMISTRY;

GENES;

EID: 66649116808     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.102.228101     Document Type: Article

References (26)

1. S. Jones, J. Mol. Biol. 287, 877 (1999). JMOBAK 0022-2836 10.1006/jmbi.1999.2659
2. K. Nadassy, S.J. Wodak, and J. Janin, Biochemistry MIRBD9 0144-0578 38, 1999 (1999). 10.1021/bi982362d
3. P.H. Von Hippel, Annu. Rev. Biophys. Biomol. Struct. 36, 79 (2007). ABBSE4 1056-8700 10.1146/annurev.biophys.34.040204.144521
4. Y. Takeda, P.D. Ross, and C.P. Mudd. Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 89, 8180 (1992). 10.1073/pnas.89.17.8180
5. H. Viadiu and A. Aggarwal. Mol. Cell 5, 889 (2000). MOCEFL 1097-2765 10.1016/S1097-2765(00)80329-9
6. C.G. Kalodimos, Science 305, 386 (2004). SCIEAS 0036-8075 10.1126/science.1097064
7. J. Gorman and E.C. Greene, Nat. Struct. Mol. Biol. 15, 768 (2008). 1545-9993 10.1038/nsmb.1441
8. I. Bonnet, Nucleic Acids Res. NARHAD 0305-1048 36, 4118 (2008). 10.1093/nar/gkn376
9. J.-P. Hansen and H. Löwen, Annu. Rev. Phys. Chem. 51, 209 (2000). ARPLAP 0066-426X 10.1146/annurev.physchem.51.1.209
10. V. Dahirel, Phys. Chem. Chem. Phys. 10, 5147 (2008). PPCPFQ 1463-9076 10.1039/b806315j
11. V. Dahirel, Phys. Rev. E PLEEE8 1539-3755 76, 040902(R) (2007). 10.1103/PhysRevE.76.040902
12. V. Dahirel, J. Chem. Phys. 127, 095101 (2007). JCPSA6 0021-9606 10.1063/1.2767626
13. H. Ohshima, Colloid Polym. Sci. CPMSB6 0303-402X 253, 150 (1975). 10.1007/BF01775681
14. F. Paillusson, M. Barbi, and J.M. Victor, arXiv:0902.1457v1.
15. S. Bhattacharjee and M. Elimelech, J. Colloid Interface Sci. 193, 273 (1997). JCISA5 0021-9797 10.1006/jcis.1997.5076
16. D. Ben-Yaakov, Europhys. Lett. 79, 48002 (2007). EULEEJ 0295-5075 10.1209/0295-5075/79/48002
17. S. Jones, Nucleic Acids Res. NARHAD 0305-1048 31, 7189 (2003). 10.1093/nar/gkg922
18. E.W. Stawiski, L.M. Gregoret, and Y. Mandel-Gutfreund, J. Mol. Biol. 326, 1065 (2003). JMOBAK 0022-2836 10.1016/S0022-2836(03)00031-7
19. J. Sun, Biophys. J. 84, 3317 (2003). BIOJAU 0006-3495 10.1016/S0006-3495(03)70056-3
20. D. Tareste, Biophys. J. 83, 3675 (2002). BIOJAU 0006-3495 10.1016/S0006-3495(02)75367-8
21. Y. Chen, Nucleic Acids Res. NARHAD 0305-1048 32, 5147 (2004). 10.1093/nar/gkh785
22. I. Eliazar, T. Koren, and J. Klafter, J. Phys. Condens. Matter JCOMEL 0953-8984 19, 065140 (2007). 10.1088/0953-8984/19/6/065140
23. B. van den Broek, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 15738 (2008). 10.1073/pnas.0804248105
24. O. Bénichou, arXiv:0901.4185v2.
25. M. Slutsky and L.A. Mirny, Biophys. J. 87, 4021 (2004). BIOJAU 0006-3495 10.1529/biophysj.104.050765
26. M. Barbi, J. Biol. Phys. JBPHBZ 0092-0606 30, 203 (2004). 10.1023/B:JOBP.0000046728.51620.14