Torque and dynamics of linking number relaxation in stretched supercoiled DNA

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 76, Issue 2, 2007, Pages

  Marko, John F ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; FREE ENERGY; FRICTION; MICROMECHANICS; TORQUE;

LINKING NUMBER RELAXATION; SUPERCOILING;

DNA;

EID: 34548403896     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.76.021926     Document Type: Article

References (49)

1. S. Smith, L. Finzi, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.1439819 258, 1122 (1992).
2. C. Bustamante, J. F. Marko, S. Smith, and E. D. Siggia, Science SCIEAS 0036-8075 10.1126/science.8079175 265, 1599 (1994).
3. A. V. Vologodskii, Macromolecules MAMOBX 0024-9297 10.1021/ma00098a016 27, 5623 (1994).
4. T. Odijk, Macromolecules MAMOBX 0024-9297 10.1021/ma00124a044 28, 7016 (1995).
5. J. F. Marko and E. D. Siggia, Macromolecules MAMOBX 0024-9297 10.1021/ma00130a008 28, 8759 (1995).
6. T. R. Strick, J.-F. Allemand, D. Bensimon, A. Bensimon, and V. Croquette, Science SCIEAS 0036-8075 10.1126/science.271.5257.1835 271, 1835 (1996).
7. T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, Biophys. J. BIOJAU 0006-3495 74, 2016 (1998).
8. T. Strick, J. F. Allemand, D. Bensimon, R. Lavery, and V. Croquette, Physica A PHYADX 0378-4371 10.1016/S0378-4371(98)00540-8 263, 392 (1999).
9. T. R. Strick, J.-F. Allemand, V. Croquette, and D. Bensimon, Prog. Biophys. Mol. Biol. PBIMAC 0079-6107 10.1016/S0079-6107(00)00018-3 74, 115 (2000).
10. T. R. Strick, V. Croquette, and D. Bensimon, Nature (London) NATUAS 0028-0836 10.1038/35009144 404, 901 (2000).
11. N. J. Crisona, T. R. Strick, D. Bensimon, V. Croquette, and N. R. Cozzarelli, Genes Dev. GEDEEP 0890-9369 10.1101/gad.838900 14, 2881-2892 (2000).
12. N. H. Dekker, V. V. Rybenkov, M. Duguet, N. J. Crisona, N. R. Cozzarelli, D. Bensimon, and V. Croquette, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.132378799 99, 12126 (2002).
13. N. H. Dekker, T. Viard, C. B. de la Tour, M. Duguet, D. Bensimon, and V. Croquette, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(03)00320-6 329, 271 (2003).
14. D. A. Koster, V. Croquette, C. Dekker, S. Shuman, and N. H. Dekker, Nature (London) NATUAS 0028-0836 10.1038/nature03395 434, 671 (2005).
15. J. Gore, Z. Bryant, M. D. Stone, M. N. Nollmann, N. R. Cozzarelli, and C. Bustamante, Nature (London) NATUAS 0028-0836 10.1038/nature04319 439, 100 (2006).
16. J. F. Marko and E. D. Siggia, Science SCIEAS 0036-8075 10.1126/science.8036491 265, 506 (1994).
17. J. F. Marko and E. D. Siggia, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.52.2912 52, 2912 (1995).
18. J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.55.1758 55, 1758 (1997).
19. B. Fain, J. Rudnick, and S. Ostlund, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.55.7364 55, 7364 (1997).
20. J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.57.2134 57, 2134 (1998).
21. S. Kutter and E. M. Terentjev, Eur. Phys. J. B EPJBFY 1434-6028 10.1007/s100510170189 21, 455 (2001);
22. S. Kutter, Ph.D. thesis, University of Cambridge, U.K., 2002.
23. N. Clauvelin, S. Neukirch, and B. Audoly, in Proceedings of the Third International Conference on Multiscale Materials Modeling, edited by, P. Gumbsch, (Fraunhofer IRB Verlag, Freiburg, Germany, 2006), pp. 605-608.
24. S. Neukirch, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93. 198107 93, 198107 (2004).
25. J. F. Marko and A. Vologodskii, Biophys. J. BIOJAU 0006-3495 10.1007/s004220050168 73, 123-132 (1997).
26. J. F. Léger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J. F. Marko, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.1066 83, 1066 (1999).
27. Z. Bryant, M. D. Stone, J. Gore, S. B. Smith, N. R. Cozzarelli, and C. Bustamante, Nature (London) NATUAS 0028-0836 10.1038/nature01810 424, 338 (2003).
28. C. Deufel, S. Forth, C. R. Simmons, S. Dejgosha, and M. D. Wang, Nat. Methods ZZZZZZ 1548-7091 4, 223 (2007).
29. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(91)90745- R 217, 413 (1991).
30. A. V. Vologodskii, S. D. Levene, K. V. Klenin, M. Frank-Kamenetskii, and N. R. Cozzarelli, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(92)90533-P 227, 1224 (1992).
31. V. V. Rybenkov, A. V. Vologodkskii, and N. R. Cozzarelli, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/25.7.1412 25, 1412 (1997).
32. J. D. Moroz and P. Nelson, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.26.14418 94, 14418 (1997).
33. J. D. Moroz and P. Nelson, Macromolecules MAMOBX 0024-9297 10.1021/ma971804a 31, 6333 (1998).
34. J. F. Allemand, D. Bensimon, and V. Croquette, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.24.14152 95, 14152 (1998).
35. A. Sarkar, J. F. Léger, D. Chatenay, and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.63.051903 63, 051903 (2001).
36. L. D. Landau and E. M. Lifshitz, Theory of Elasticity (Pergamon, New York, 1986), Chap..
37. V. Rossetto, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2004-10306-3 69, 142 (2005).
38. J. F. Marko, in Proceedings of the Les Houches Summer School of Theoretical Physics, LXXXII, August 2-27, 2004, Multiple Aspects of DNA and RNA from Biophysics to Bioinformatics, edited by, D. Chatenay, (Elsevier, San Diego, CA, 2005), pp. 248-250.
39. A. E. H. Love, A Treatise on the Mathematical Theory of Elasticity (Dover, New York, 1944), pp. 417-419.
40. S. Cocco, J. Yan, J. F. Léger, D. Chatenay, and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.011910 70, 011910 (2004).
41. E. Evans and K. Ritchie, Biophys. J. BIOJAU 0006-3495 72, 1541-1555 (1997).
42. J. F. Marko, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i1997-00223-5 38, 183 (1997).
43. T. Lionnet, S. Joubaud, R. Lavery, D. Bensimon, and V. Croquette, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.178102 96, 178102 (2006).
44. J. Gore, Z. Bryant, M. Nollmann, M. U. Le, N. R. Cozzarelli, and C. Bustamante, Nature (London) NATUAS 0028-0836 10.1038/nature04974 442, 836-839 (2006).
45. S. Cocco, J. F. Marko, R. Monasson, A. Sarkar, and J. Yan, Eur. Phys. J. E EPJSFH 1292-8941 10.1140/epje/i2002-10113-2 10, 249 (2003).
46. J. Yan and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.011905 68, 011905 (2003).
47. G. Charvin, T. R. Strick, D. Bensimon, and V. Croquette, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.060202 89, 384 (2005).
48. B. Schnurr, C. Vorgias, and J. Stavans, Biophys. Rev. Lett. 1, 29 (2006).
49. D. A. Koster, K. Palle, E. S. M. Bot, M. A. Bjornsti, N. H. Dekker, Nature NATUAS 0028-0836 448, 213 (2007).