DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism

Journal of Physical Chemistry B

Volumn 116, Issue 38, 2012, Pages 11616-11625

  Matek, Christian ^a   Ouldridge, Thomas E ^a   Levy, Adam ^a   Doye, Jonathan P K ^a   Louis, Ard A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MONTE CARLO METHODS; NUCLEATION; TORSIONAL STRESS;

BUBBLE FLUCTUATIONS; CENTER OF SYMMETRY; COARSE GRAINED MODELS; COOPERATIVE MECHANISMS; DIRECT SIMULATION; INVERTED REPEAT; MONTE CARLO SIMULATION; SUPERHELICAL DENSITY; UMBRELLA SAMPLING;

DNA SEQUENCES;

EID: 84866875448     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp3080755     Document Type: Article

References (56)

1. Watson, J. D.; Crick, F. H. Nature 1953, 171, 737-738
2. Bates, A. D.; Maxwell, A. DNA Topology; Oxford University Press: Oxford, U.K., 2005.
3. Drolet, M. Mol. Microbiol. 2006, 59, 723-730
4. Sinden, R. R. DNA Structure and Function; Academic Press Inc.: New York, 1994.
5. Benham, C. J.; Savitt, A. G.; Bauer, W. R. J. Mol. Biol. 2002, 316, 563-581
6. Bikard, D.; Loot, C.; Baharoglu, Z.; Mazel, D. Microbiol. Mol. Biol. Rev. 2010, 74, 570-588
7. Calladine, C. R.; Drew, H. R.; Luisi, B. F.; Travers, A. A. Understanding DNA, 3 rd ed.; Elsevier Press: New York, 2004.
8. Mizuuchi, K.; Mizuuchi, M.; Gellert, M. J. Mol. Biol. 1982, 156, 229-243
9. Platt, J. R. Proc. Natl. Acad. Sci. U.S.A. 1955, 41, 181-183
10. Lilley, D. M. J. Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 6468-6472
11. Panayotatos, N.; Wells, R. D. Nature 1981, 289, 466-470
12. Lilley, D. M. J. Nucleic Acids Res. 1985, 13, 1443-1465
13. Lilley, D. M. J.; Gough, G. W.; Hallam, L. R.; Sullivan, K. M. Biochimie 1985, 67, 697-706
14. Lilley, D. M.; Hallam, L. R. J. Mol. Biol. 1984, 180, 179-200
15. Sinden, R. R.; Pettijohn, D. E. J. Biol. Chem. 1984, 259, 6593-6600
16. Courey, A. J.; Wang, J. C. Cell 1983, 33, 817-829
17. Sinden, R. R.; Broyles, S. S.; Pettijohn, D. E. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 1797-1801
18. Dayn, A.; Malkhosyan, S.; Duzhy, D.; Lyamichev, V.; Panchenko, Y.; Mirkin, S. J. Bacteriol. 1991, 173, 2658-2664
19. Horwitz, M. S.; Loeb, L. A. Science 1988, 241, 703-705
20. Noirot, P.; Bargonetti, J.; Novick, R. P. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 8560-8564
21. Zheng, G. X.; Kochel, T.; Hoepfner, R. W.; Timmons, S. E.; Sinden, R. R. J. Mol. Biol. 1991, 221, 107-122
22. Zheng, G.; Ussery, D. W.; Sinden, R. R. J. Mol. Biol. 1991, 221, 122-129
23. Gierer, A. Nature 1966, 212, 1480-1481
24. Coté, A. G.; Lewis, S. M. Mol. Cell 2008, 31, 800-812
25. Ward, G. K.; el Deen, A. S.; Zannis-Hadjopoulos, M.; Price, G. B. Exp. Cell Res. 1991, 195, 92-98
26. Brázda, V.; Laister, R. C.; Jagelská, E. B.; Arrowsmith, C. BMC Mol. Biol. 2011, 12, 33
27. Oussatcheva, E. A.; Pavlicek, J.; Sankey, O. F.; Sinden, R. R.; Lyubchenko, Y. L.; Potaman, V. N. J. Mol. Biol. 2004, 338, 735-743
28. Shlyakhtenko, L. S.; Hsieh, P.; Grigoriev, M.; Potaman, V. N.; Sinden, R. R.; Lyubchenko, Y. L. J. Mol. Biol. 2000, 296, 1169-1173
29. Seeman, N. C.; Kallenbach, N. R. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 53-86
30. Shlyakhtenko, L. S.; Potaman, V. N.; Sinden, R. R.; Lyubchenko, Y. L. J. Mol. Biol. 1998, 280, 61-72
31. Kapanidis, A. N.; Strick, T. Trends Biochem. Sci. 2009, 34, 234-243
32. Tinoco, I.; Gonzalez, R. L. Genes Dev. 2011, 25, 1205-1231
33. Ramreddy, T.; Sachidanandam, R.; Strick, T. R. Nucleic Acids Res. 2011, 39, 4275-4283
34. Charvin, G.; Allemand, J.-F.; Strick, T. R.; Bensimon, D.; Croquette, V. Contemp. Phys. 2004, 45, 383-403
35. Lankaš, F. In Innovations in Biomolecular Modeling and Simulation; Schlick, T., Ed.; RSC Publishing: London, U.K., 2012; Vol. 2, Chapter Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale, pp 3-32.
36. de Pablo, J. J. Annu. Rev. Phys. Chem. 2011, 62, 555-574
37. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. J. Chem. Phys. 2011, 134, 085101
38. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Phys. Rev. Lett. 2010, 104, 178101
39. De Michele, C.; Rovigatti, L.; Bellini, T.; Sciortino, F. Soft Matter 2012, 8, 8388-8398
40. Romano, F.; Hudson, A.; Doye, J. P. K.; Ouldridge, T. E.; Louis, A. A. J. Chem. Phys. 2012, 136, 215102
41. Lilley, D. M. J. Trends Genet. 1988, 4, 111-114
42. White, J. H. Am. J. Math. 1969, 91, 693-728
43. Champion, K.; Higgins, N. P. J. Bacteriol. 2007, 189, 5839-5849
44. Randall, G. L.; Zechiedrich, L.; Pettitt, B. M. Nucleic Acids Res. 2009, 37, 5568-5577
45. Strick, T. R.; Allemand, J. F.; Bensimon, D.; Croquette, V. Biophys. J. 1998, 74, 2016-2028
46. Harris, S. A.; Laughton, C. A.; Liverpool, T. B. Nucleic Acids Res. 2008, 36, 21-29
47. Pearson, C. E.; Zorbas, H.; Price, G. B.; Zannis-Hadjopoulos, M. J. Cell. Biochem. 1996, 63, 1-22
48. Whitelam, S.; Geissler, P. L. J. Chem. Phys. 2007, 127, 154101
49. Whitelam, S.; Feng, E. H.; Hagan, M. F.; Geissler, P. L. Soft Matter 2009, 5, 1251-1262
50. Ouldridge, T. E. Ph.D. thesis, University of Oxford, 2011; see http://tinyurl.com/7ycbx7c.
51. Frenkel, D.; Smit, B. Understanding Molecular Simulation; Academic Press Inc.: New York, 2001.
52. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1992, 13, 1011-1021
53. Fye, R. M.; Benham, C. J. Phys. Rev. E 1999, 59, 3408-3426
54. Jeon, J.-H.; Adamcik, J.; Dietler, G.; Metzler, R. Phys. Rev. Lett. 2010, 105, 208101
55. SantaLucia, J.; Hicks, D. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 415-440
56. Šulc, P.; Romano, F.; Ouldridge, T. E.; Rovigatti, L.; Doye, J. P. K.; Louis, A. A. Sequence-Dependent Thermodynamics of a Coarse-Grained DNA Model. J. Chem. Phys. 2012, arXiv:1207.3391v1, in press.