Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

Journal of Chemical Physics

Volumn 136, Issue 4, 2012, Pages

  Sivak, David A ^a,b   Geissler, Phillip L ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRING; DEHYBRIDIZATION; DNA BENDING; DOUBLE STRANDED DNA; FORCE-EXTENSION; LOCAL FLEXIBILITY; LONG CHAINS; MICROSCOPIC MODELS; MONTE CARLO SIMULATION; SHORTER CHAINS; SINGLE-MOLECULE; WORM-LIKE CHAIN MODELS; WORMLIKE CHAIN;

ELASTICITY; MELTING; MOLECULES; MONTE CARLO METHODS; SAMPLING; THERMODYNAMICS;

CYCLIZATION;

DNA;

ARTICLE; BASE PAIRING; CHEMISTRY;

BASE PAIRING; DNA;

EID: 84861147704     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3679654     Document Type: Article

References (44)

1. C. Bustamante, S. B. Smith, J. T. Liphardt, and D. Smith, Curr. Opin. Struct. Biol. 10, 279 (2000). 10.1016/S0959-440X(00)00085-3
2. S. B. Smith, Y. Cui, and C. Bustamante, Science 271, 795 (1996). 10.1126/science.271.5250.795
3. C. Bustamante, Z. Bryant, and S. B. Smith, Nature (London) 421, 423 (2003). 10.1038/nature01405
4. D. Crothers, J. Drak, J. Kahn, and S. Levene, Methods Enzymol. 212, 3 (1992). 10.1016/0076-6879(92)12003-9
5. J. Perez-Martin and V. de Lorenzo, Annu. Rev. Microbiol. 51, 593 (1997). 10.1146/annurev.micro.51.1.593
6. T. J. Richmond and C. A. Davey, Nature (London) 423, 145 (2003). 10.1038/nature01595
7. P. A. Rice, S. W. Yang, K. Mizuuchi, and H. A. Nash, Cell 87, 1295 (1996). 10.1016/S0092-8674(00)81824-3
8. H. G. Garcia, P. Grayson, L. Han, M. Inamdar, J. Kondev, P. C. Nelson, R. Phillips, J. Widom, and P. A. Wiggins, Biopolymers 85, 115 (2007). 10.1002/bip.20627
9. C. A. Mirkin, R. Letsinger, R. Mucic, and J. Storhoff, Nature (London) 382, 607 (1996). 10.1038/382607a0
10. A. Fu, C. M. Micheel, J. Cha, H. Chang, H. Yang, and A. P. Alivisatos, J. Am. Chem. Soc. 126, 10832 (2004). 10.1021/ja046747x
11. S. Claridge, A. J. Mastroianni, Y. Au, H. Liang, C. M. Micheel, J. M. J. Frechet, and A. P. Alivisatos, J. Am. Chem. Soc. 130, 9598 (2008). 10.1021/ja8026746
12. H. Dietz, S. M. Douglas, and W. M. Shih, Science 325, 725 (2009). 10.1126/science.1174251
13. S. Y. Park, A. K. R. Lytton-Jean, B. Lee, S. Weigand, G. C. Schatz, and C. A. Mirkin, Nature (London) 451, 553 (2008). 10.1038/nature06508
14. P. A. Wiggins, T. van der Heijden, F. Moreno-Herrero, A. J. Spakowitz, R. S. Phillips, J. Widom, C. Dekker, and P. C. Nelson, Nat. Nanotechnol. 1, 137 (2006). 10.1038/nnano.2006.63
15. C. Yuan, H. Chen, X. W. Lou, and L. A. Archer, Phys. Rev. Lett. 100, 018102 (2008). 10.1103/PhysRevLett.100.018102
16. T. E. Cloutier and J. Widom, Mol. Cell. 14, 355 (2004). 10.1016/S1097-2765(04)00210-2
17. Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. V. Vologodskii, Proc. Natl. Acad. Sci. U.S.A. 102, 5397 (2005). 10.1073/pnas.0500983102
18. P. A. Wiggins and P. C. Nelson, Phys. Rev. E 73, 031906 (2006). 10.1103/PhysRevE.73.031906
19. J. Yan and J. F. Marko, Phys. Rev. Lett. 93, 108108 (2004). 10.1103/PhysRevLett.93.108108
20. J. Yan, R. Kawamura, and J. F. Marko, Phys. Rev. E 71, 061905 (2005). 10.1103/PhysRevE.71.061905
21. P. A. Wiggins, R. S. Phillips, and P. C. Nelson, Phys. Rev. E 71, 021909 (2005). 10.1103/PhysRevE.71.021909
22. J. Yan and J. F. Marko, Phys. Rev. E 68, 011905 (2003). 10.1103/PhysRevE.68.011905
23. M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, Biophys. J. 72, 1335 (1997). 10.1016/S0006-3495(97)78780-0
24. W. H. Taylor and P. J. Hagerman, J. Mol. Biol. 212, 363 (1990). 10.1016/0022-2836(90)90131-5
25. R. A. Forties, R. Bundschuh, and M. G. Poirier, Nucleic Acids Res. 37, 4580 (2009). 10.1093/nar/gkp442
26. J. P. Peters and L. J. Maher III, Q. Rev. Biophys. 43, 23 (2010). 10.1017/S0033583510000077
27. R. R. Cheng, T. Uzawa, K. W. Plaxco, and D. E. Makarov, Biophys. J. 99, 3959 (2010). 10.1016/j.bpj.2010.11.017
28. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959). 10.1063/1.1730390
29. J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007). 10.1103/PhysRevLett.99.088103
30. A. J. Mastroianni, D. A. Sivak, P. L. Geissler, and A. P. Alivisatos, Biophys. J. 97, 1408 (2009). 10.1016/j.bpj.2009.06.031
31. J. SantaLucia, Proc. Natl. Acad. Sci. U.S.A. 95, 1460 (1998). 10.1073/pnas.95.4.1460
32. D. P. Landau, S. Tsai, and M. Exler, Am. J. Phys. 72, 1294 (2004). 10.1119/1.1707017
33. J. F. Allemand, S. Cocco, N. Douarche, and G. Lia, Eur. Phys. J. E 19, 293 (2006). 10.1140/epje/i2005-10073-y
34. H. Yamakawa and W. Stockmayer, J. Chem. Phys. 57, 2843 (1972). 10.1063/1.1678675
35. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, Biophys. J. 86, 2530 (2004). 10.1016/S0006-3495(04)74308-8
36. J. Shimada and H. Yamakawa, Macromolecules 17, 689 (1984). 10.1021/ma00134a028
37. Q. Du, A. Kotlyar, and A. V. Vologodskii, Nucleic Acids Res. 36, 1120 (2008). 10.1093/nar/gkm1125
38. J. E. Mertz and R. W. Davis, Proc. Natl. Acad. Sci. U.S.A. 69, 3370 (1972). 10.1073/pnas.69.11.3370
39. Y. Lu, B. Weers, and N. C. Stellwagen, Biopolymers 61, 261 (2001). 10.1002/bip.10151
40. C. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. 94, 6185 (1997). 10.1073/pnas.94.12.6185
41. W. K. Olson, A. A. Gorin, X.-J. Lu, L. Hock, and V. B. Zhurkin, Proc. Natl. Acad. Sci. U.S.A. 95, 11163 (1998). 10.1073/pnas.95.19.11163
42. A. Krueger, E. Protozanova, and M. D. Frank-Kamenetskii, Biophys. J. 90, 3091 (2006). 10.1529/biophysj.105.078774
43. M. C. Williams, J. R. Wenner, I. Rouzina, and V. A. Bloomfield, Biophys. J. 80, 1932 (2001). 10.1016/S0006-3495(01)76163-2
44. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, 684 (1993). 10.1103/PhysRevE.47.684