Statistics of loop formation along double helix DNAs

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

Volumn 71, Issue 6, 2005, Pages

  Yan, Jie ^a   Kawamura, Ryo ^a   Marko, John F ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE HELIX DNAS; DOUBLE-STRANDED DNA MOLECULE (DSDNA); LOOP FORMATION;

BOUNDARY CONDITIONS; DEFECTS; ELASTICITY; MATRIX ALGEBRA; POLYMERS;

DNA;

DNA;

CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELASTICITY; MECHANICAL STRESS; STATISTICAL MODEL; TENSILE STRENGTH;

COMPUTER SIMULATION; DNA; ELASTICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; STRESS, MECHANICAL; TENSILE STRENGTH;

EID: 27944487890     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.71.061905     Document Type: Article

References (49)

1. J. Dekker, Trends Biochem. Sci. TBSCDB 0167-7640 10.1016/S0968-0004(03) 00089-6 28, 277 (2003).
2. K. Rippe, P. H. von Hippel, and J. Langowski, Trends Biochem. Sci. TBSCDB 0167-7640 10.1016/S0968-0004(00)89117-3 20, 500 (1995).
3. S. Oehler, M. Amouyal, P. Kolkhof, B. Wilcken-Bergmann, and B. Muller-Hill, EMBO J. EMJODG 0261-4189 13, 3348 (1994).
4. Y. Chen, and P. A. Rice, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.32.110601.141732 32, 135 (2003).
5. B. M. Weiner, and N. Kleckner, Cell CELLB5 0092-8674 10.1016/0092- 8674(94)90438-3 77, 977 (1994).
6. W. F. Marshall, A. Straight, J. F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A. W. Murray, D. A. Agard, and J. W. Sedat, Curr. Biol. CUBLE2 0960-9822 10.1016/S0960-9822(06)00412-X 7, 930 (1997).
7. R. Scleif, Annu. Rev. Biochem. ARBOAW 0066-4154 10.1146/annurev.biochem. 61.1.199 61, 199 (1992).
8. S. E. Halford, A. J. Welsh, and M. D. Szczelkun, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.33.110502.132711 33, 1 (2004).
9. J. M. Vilar and S. Leibler, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(03)00764-2 331, 981 (2003).
10. M. Geanacopoulos, G. Vasmatzis, V. B. Zhurkin, and S. Adhya, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/87595 8, 432 (2001);
11. S. Semsey, M. Y. Tolstorukov, K. Virnik, V. B. Zhurkin, and S. Adhya, Genes Dev. GEDEEP 0890-9369 10.1101/gad.1209404 18 1898 (2004).
12. V. L. Brandt and D. B. Roth, Curr. Opin. Immunol. COPIEL 0952-7915 14, 224 (2002).
13. T. J. Richmond and C. A. Davey, Nature (London) NATUAS 0028-0836 10.1038/nature01595 423, 145 (2003).
14. B. M. Ali, R. Amit, I. Braslavsky, A. B. Oppenhein, O. Gileadi, and J. Stavans, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.181029198 98, 10658 (2001).
15. R. Amit, A. B. Oppenheim, and J. Stavans, Biophys. J. BIOJAU 0006-3495 84, 2467 (2003).
16. J. van Noort, S. Vebrugge, N. Goosen, C. Dekker, and R. T. Dame, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0308230101 101, 6969 (2004).
17. D. Skoko, B. Wong, R. C. Johnson, and J. F. Marko, Biochemistry BICHAW 0006-2960 10.1021/bi048428o 43, 13867 (2004).
18. L. Finzi and J. Gelles, Science SCIEAS 0036-8075 267, 378 (1995).
19. G. Lia, D. Bensimon, V. Croquette, J. F. Allemand, D. Dunlap, D. E. Lewis, S. Adhya, and L. Finzi, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2034851100 100, 11373 (2003).
20. J. Yan, D. Skoko, and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.011905 70, 011905 (2004).
21. C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00085-3 10, 279 (2000).
22. J. Liphardt, B. Onoa, S. B. Smith, I. J. R. Tinoco, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.1058498 292, 733 (2002).
23. D. Shore, J. Langowski, and R. L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 79, 4833 (1981).
24. P. J. Hagerman, Annu. Rev. Biophys. Biophys. Chem. ARBCEY 0883-9182 10.1146/annurev.bb.17.060188.001405 17, 265 (1988).
25. Y. Zhang and D. M. Crothers, Biophys. J. BIOJAU 0006-3495 84, 136 (2003).
26. Y. Zhang and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0530189100 100, 3161 (2003).
27. H. Arthanari, K. Wojtuszewski, I. Mukerji, and P. H. Bolton, Biophys. J. BIOJAU 0006-3495 86, 1625 (2004).
28. T. E. Cloutier and J. Widom, Mol. Cell MOCEFL 1097-2765 10.1016/S1097-2765(04)00210-2 14, 355 (2004).
29. H. Yamakawa and W. H. Stockmayer, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1678675 57, 2843 (1972).
30. J. Shimada and H. Yamakawa, Macromolecules MAMOBX 0024-9297 10.1021/ma00134a028 17, 689 (1984).
31. A. Podtelezhnikov and A. Vologodskii, Macromolecules MAMOBX 0024-9297 10.1021/ma970391a 30, 6668 (1997).
32. J. Yan and J. F. Marko, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.108108 93, 108108 (2004).
33. P. A. Wiggins, R. Phillips, and P. C. Nelson Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71.021909 71, 021909 (2005).
34. J. Yan and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.011905 68, 011905 (2003).
35. M. D. Wang, M. J. Schnitzer, H. Yin, R. Landick, J. Gelles, and S. M. Block, Science SCIEAS 0036-8075 10.1126/science.282.5390.902
36. T. Strick, J. Allemand, V. Croquette, and D. Bensimon, Prog. Biophys. Mol. Biol. PBIMAC 0079-6107 10.1016/S0079-6107(00)00018-3 74, 115 (2000).
37. S. B. Smith, Y. Cui, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.274.5288.795 271, 795 (1996).
38. C. Storm and P. C. Nelson, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.67.051906 67, 051906 (2003).
39. M. Doi and S. F. Edwards, Theory of Polymer Dynamics (New York, Oxford, 1985).
40. J. Santalucia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.4.1460 95, 1460 (1998).
41. D. H. Matthews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.2700 288, 911 (1999), see Table 17.
42. 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).
43. J. F. Marko and E. D. Siggia, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.52.2912 52, 2912 (1995).
44. J. F. Marko and E. D. Siggia, Biophys. J. BIOJAU 0006-3495 73, 2173 (1997).
45. S. Sankararaman and J. F. Marko, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71.021911 71, 021911 (2005).
46. P. Ranjith, P. B. Sunil Kumar, and G. I. Menon, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.138102 94, 138102 (2005).
47. D. M. Crothers, T. E. Haran, and J. G. Nadeau, J. Biol. Chem. JBCHA3 0021-9258 265, 7093 (1990).
48. A. J. Spakowitz and Z. G. Wang, Macromolecules MAMOBX 0024-9297 10.1021/ma049958v 37, 5814 (2004).
49. L. Dai and F. Liu, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1610447 119, 8124 (2003).