Overstretching and force-driven strand separation of double-helix DNA

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 70, Issue 1, 2004, Pages 18-

  Cocco, Simona ^a   Yan, Jie ^b   Léger, Jean Francois ^a   Chatenay, Didier ^a   Marko, John F ^b  

^a CNRS   (France)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; DNA; ELASTICITY; FREE ENERGY; FUNCTIONS; HYSTERESIS; INTEGRATION; IONIC STRENGTH; MELTING; STATISTICAL MECHANICS; THERMAL EFFECTS;

FREE ENERGY BARRIERS; LOGARITHMIC LOOP INTERACTION; POLYNUCLEOTIDE STRANDS;

BIOTECHNOLOGY;

DNA; SODIUM CHLORIDE;

ARTICLE; BASE PAIRING; BODY FLUID; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; DNA DAMAGE; DNA DENATURATION; ELASTICITY; EVALUATION; KINETICS; MECHANICAL STRESS; METHODOLOGY; MICROMANIPULATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SOLUTION AND SOLUBILITY; VALIDATION STUDY;

BASE PAIRING; BASE SEQUENCE; BODY FLUIDS; COMPUTER SIMULATION; DNA; DNA DAMAGE; ELASTICITY; KINETICS; MICROMANIPULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SODIUM CHLORIDE; SOLUTIONS; STRESS, MECHANICAL;

EID: 42749104291     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.70.011910     Document Type: Article

References (45)

1. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J.-L. Viovy, D. Chatenay, and F. Caron, ScienceSCIEAS0036-807510.1126/science.271.5250.792 271, 792 (1996).
2. S. B. Smith, Y. J. Cui, and C. Bustmante, ScienceSCIEAS0036-807510.1126/science.271.5250.795 271, 795 (1996).
3. C. G. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 94, 61850 (1997).
4. M. Rief, H. Clausen-Schaumann, and H. E. Gaub, Nat. Struct. Biol.NSBIEW1072-836810.1038/7582 6, 346 (1999).
5. J.-F. Leger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J. F. Marko, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.83.1066 83, 1066 (1999).
6. H. Clausen-Schaumann, M. Rief, C. Tolksdorf, and H. E. Gaub, Biophys. J.BIOJAU0006-3495 78, 1997 (2001).
7. J.-F. Leger, Ph.D. thesis, l’Université Louis Pasteur Strasbourg I, 2000.
8. I. Rouzina and V. A. Bloomfield, Biophys. J.BIOJAU0006-3495 80, 882 (2001).10.1016/S0006-3495(01)76067-5
9. I. Rouzina and V. A. Bloomfield, Biophys. J.BIOJAU0006-3495 80, 894 (2001).10.1016/S0006-3495(01)76068-7
10. J. R. Wenner, M. C. Williams, I. Rouzina, and V. A. Bloomfield, Biophys. J.BIOJAU0006-3495 82, 3160 (2002).10.1016/S0006-3495(02)75658-0
11. U. Bockelmann, B. Essevaz-Roulet, and F. Heslot, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 94, 11?935 (1997).10.1073/pnas.94.1.11
12. C. Bustamante, D. Smith, and S. Smith, Curr. Opin. Struct. Biol.COSBEF0959-440X10.1016/S0959-440X(00)00085-3 10, 279 (2000).
13. U. Bockelmann, B. Essevaz-Roulet, and F. Heslot, Biophys. J.BIOJAU0006-3495 82, 1537 (2002).10.1016/S0006-3495(02)75506-9
14. J. SantaLucia, Jr., Proc. Natl. Acad. Sci. U.S.A.PNASA60027-842410.1073/pnas.95.4.1460 95, 1460 (1998).
15. A. Yu. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules (AIP Press, Woodbury, NY, 1994), pp. 302–312.
16. S. Cocco, J. F. Marko, and R. Monasson, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-842410.1073/pnas.151257598 98, 8608 (2001).
17. S. Cocco, R. Monasson, and J. F. Marko, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.66.051914 66, 051914 (2002).
18. S. Cocco, J. F. Marko, and R. Monasson, Eur. J. Phys.EJPHD40143-0807 10, 153 (2003).
19. A. Sarkar, J.-F. Leger, D. Chatenay, and J. F. Marko, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.63.051903 63, 051903 (2001).
20. A. Lebrun and R. Lavery, Nucleic Acids Res.NARHAD0305-104810.1093/nar/24.12.2260 24, 2260 (1996).
21. P. Cizeau and J.-L. Viovy, BiopolymersBIPMAA0006-352510.1002/(SICI)1097-0282(19971005)42:4<383::AID-BIP1>3.0.CO;2-M 42, 383 (1997).
22. C. Storm and P. C. Nelson, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.67.051906 67, 051906 (2003).
23. J.-F. Allemand, D. Bensimon, R. Lavery, and V. Croquette, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 95, 14?152 (1998).
24. D. Lubensky and D. R. Nelson, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.85.1572 85, 1572 (2000).
25. D. Lubensky and D. R. Nelson, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.65.031917 65, 031917 (2002).
26. U. Gerland, R. Bundschuh, and T. Hwa, Biophys. J.BIOJAU0006-3495 81, 1324 (2001).10.1016/S0006-3495(01)75789-X
27. M. Prentiss, D. Lubensky, and D. R. Nelson, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-842410.1073/pnas.262789199100, 1694 (2003).
28. J. F. Marko and E. D. Siggia, MacromoleculesMAMOBX0024-9297 28, 8759 (1995).10.1021/ma00130a008
29. M.-N. Dessinges, B. Maier, Y. Zhang, M. Peliti, D. Bensimon, and V. Croquette, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.89.248102 89, 248102 (2002).
30. B. Maier, D. Bensimon, and V. Croquette, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 97, 12?002 (2000).
31. Y. Zhang, H. J. Zhou, and Z. C. Ou-Yang, Biophys. J.BIOJAU0006-3495 81, 1133 (2001).10.1016/S0006-3495(01)75770-0
32. K. J. Breslauer, R. Frank, H. Blocker, and L. A. Marky, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 83, 3746 (1986).10.1073/pnas.83.11.3746
33. J.-F. Leger, G. Romano, J. Robert, L. Bourdieu, D. Chatenay, and J. F. Marko, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 95, 12?295 (1998).
34. D. H. Turner, Curr. Opin. Struct. Biol.COSBEF0959-440X10.1016/S0959-440X(96)80047-9 6, 299 (1996).
35. V. A. Bloomfield, D. M. Crothers, and I. Tinoco, Jr., Physical Chemistry of Nucleic Acids (Harper and Row, New York, 1974).
36. R. M. Wartell and A. S. Benight, Phys. Rep.PRPLCM0370-157310.1016/0370-1573(85)90060-2 126, 67 (1985).
37. J. DeMasi, S. Du, D. Lennon, and P. Traktman, J. Virol.JOVIAM0022-538X10.1128/JVI.75.21.10090-10105.2001 75, 10090 (2001).
38. S. Smith, L. Finzi, and C. Bustamante, ScienceSCIEAS0036-8075 258, 1122 (1992).10.1126/science.1439819
39. T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, Biophys. J.BIOJAU0006-3495 74, 2016 (1998).10.1016/S0006-3495(98)77908-1
40. S. Cocco, J. F. Marko, R. Monasson, A. Sarkar, and J. Yan, Eur. J. Phys.EJPHD40143-0807 10, 249 (2003).
41. P. R. Bianco, R. B. Tracy, and S. C. Kowalczykowski, Front. Biosci.FRBIF61093-4715 17, D570 (1998).
42. E. Yeramian, GeneGENED60378-111910.1016/S0378-1119(00)00300-0 255, 151 (2000).
43. G. W. Hatfield and C. J. Benham, Annu. Rev. Genet.ARVGB70066-149710.1146/annurev.genet.36.032902.111815 36, 175 (2002).
44. M. D. Wang, M. D. Schnitzer, H. Yin, R. Landick, J. Gelles, and S. M. Block, ScienceSCIEAS0036-807510.1126/science.282.5390.902 282, 902 (1998).
45. H. J. Zhou, and Z.-C. Ou-Yang, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.82.456082, 4560 (1999).