Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA

Journal of Chemical Physics

Volumn 130, Issue 14, 2009, Pages

  Kapri, Rajeev ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ATTRACTIVE SURFACES; CRITICAL END POINTS; CRITICAL VALUES; DOUBLE STRANDED DNA (DS DNA); DOUBLE-STRANDED DNAS; EXTERNAL FORCES; TRIPLE POINTS;

GENES; NUCLEIC ACIDS; PHASE DIAGRAMS;

DNA;

DNA; SINGLE STRANDED DNA;

ADSORPTION; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MECHANICAL STRESS; PHASE TRANSITION; THERMODYNAMICS;

ADSORPTION; DNA; DNA, SINGLE-STRANDED; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PHASE TRANSITION; STRESS, MECHANICAL; THERMODYNAMICS;

EID: 65249100149     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3116082     Document Type: Article

References (44)

1. J. D. Watson, T. A. Baker, S. P. Bell, A. Gann, M. Levine, and R. Losick, Molecular Biology of the Gene, 5th ed. (Pearson/Benjamin Cummings, Singapore, 2003).
2. S. M. Bhattacharjee, e-print arXiv:condmat/9912297; J. Phys. A 0305-4470 10.1088/0305-4470/33/45/101 33, L423 (2000).
3. K. L. Sebastian, Phys. Rev. E 1063-651X 10.1103/PhysRevE.62.1128 62, 1128 (2000).
4. D. Marenduzzo, A. Trovato, and A. Maritan, Phys. Rev. E 1063-651X 10.1103/PhysRevE.64.031901 64, 031901 (2001).
5. R. Kapri, S. M. Bhattacharjee, and F. Seno, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.93.248102 93, 248102 (2004).
6. D. Marenduzzo, S. M. Bhattacharjee, A. Maritan, E. Orlandini, and F. Seno, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.88.028102 88, 028102 (2001).
7. Y. Kafri, D. Mukamel, and L. Peliti, Eur. Phys. J. B 1434-6028 10.1007/s10051-002-9012-2 27, 135 (2002).
8. A. V. Tkachenko, Phys. Rev. E 1063-651X 10.1103/PhysRevE.70.051901 70, 051901 (2004).
9. D. K. Lubensky and D. R. Nelson, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.85.1572 85, 1572 (2000); D. K. Lubensky and D. R. Nelson, Phys. Rev. E 1063-651X 10.1103/PhysRevE.65.031917 65, 031917 (2002).
10. R. Kapri and S. M. Bhattacharjee, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/18/14/S06 18, S215 (2006).
11. S. M. Bhattacharjee and D. Marenduzzo, J. Phys. A 0305-4470 10.1088/0305-4470/35/26/101 35, L349 (2002).
12. D. Keller, D. Swigon, and C. Bustamante, Biophys. J. 84, 733 (2003) 0006-3495; R. M. Neumann, Biophys. J. 85, 3418 (2003). 0022-3689
13. S. M. Bhattacharjee, Europhys. Lett. 0295-5075 10.1209/epl/i2003-10107-2 65, 574 (2004).
14. S. Kumar, D. Giri, and S. M. Bhattacharjee, Phys. Rev. E 1063-651X 10.1103/PhysRevE.71.051804 71, 051804 (2005).
15. N. Singh and Y. Singh, Eur. Phys. J. E 1292-8941 10.1140/epje/i2004- 10100-7 17, 7 (2005).
16. S. Kumar and D. Giri, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.98. 048101 98, 048101 (2007).
17. J. Kierfeld, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.97.058302 97, 058302 (2006).
18. J. Z. Y. Chen, Phys. Rev. E 1063-651X 10.1103/PhysRevE.66.031912 66, 031912 (2002).
19. H. Zhou, e-print arXiv:cond-mat/0007015.
20. A. E. Allahverdyan, Zh. S. Gevorkian, C.-K. Hu, and M.-C. Wu, Phys. Rev. E 1063-651X 10.1103/PhysRevE.69.061908 69, 061908 (2004).
21. P. -M. Lam, J. C. S. Levy, and H. Huang, Biopolymers 0006-3525 10.1002/bip.10584 73, 293 (2004); P. -M. Lam and J. C. S. Levy, Biopolymers 0006-3525 10.1002/bip.20292 79, 287 (2005).
22. D. Giri and S. Kumar, Phys. Rev. E 1063-651X 10.1103/PhysRevE.73.050903 73, 050903 (2006).
23. R. Kapri and S. M. Bhattacharjee, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.98.098101 98, 098101 (2007); R. Kapri and S. M. Bhattacharjee, Physica A 384, 10 (2007). 0378-4371
24. R. Kapri and S. M. Bhattacharjee, Phys. Rev. E 1063-651X 10.1103/PhysRevE.72.051803 72, 051803 (2005).
25. E. Orlandini, M. C. Tesi, and S. G. Whittington, J. Phys. A 0305-4470 10.1088/0305-4470/37/5/005 37, 1535 (2004).
26. B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.94.22.11935 94, 11935 (1997).
27. D. Anselmetti, J. Fritz, B. Smith, and X. Fernandez-Busquets, Single Mol. 1, 53 (2000).
28. C. Danilowicz, Y. Kafri, R. S. Conroy, V. W. Coljee, J. Weeks, and M. Prentiss, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.93.078101 93, 078101 (2004).
29. W. Firshein, Annu. Rev. Microbiol. 0066-4227 10.1146/annurev.micro.43.1. 89 43, 89 (1989).
30. J. Herrick, R. Kern, S. Guha, A. Landoulsi, O. Fayet, A. Malki, and M. Kohiyama, EMBO J. 13, 4695 (1994). 0261-4189
31. T. Hoshino, T. McKenzie, S. Schmidt, T. Tanaka, and N. Sueoka, Proc. Natl. Acad. Sci. U.S.A. 84, 653 (1987). 0027-8424
32. N. Dan, Biophys. J. 71, 1267 (1996). 0006-3495
33. R. Eckel, R. Ros, A. Ros, S. D. Wilking, N. Sewald, and D. Anselmetti, Biophys. J. 85, 1968 (2003). 0006-3495
34. D. Poland and H. A. Scheraga, J. Chem. Phys. 0021-9606 10.1063/1.1727785 45, 1456 (1966).
35. A CEP is a critical point where a line of second-order transition terminates at a line of first-order transition.
36. A triple point is the intersection on a phase diagram where three phases coexist in equilibrium.
37. R. Kapri and S. M. Bhattacharjee, Europhys. Lett. 83, 68002 (2008). 0295-5075
38. S. M. Bhattacharjee and F. Seno, J. Phys. A 0305-4470 10.1088/0305-4470/34/33/302 34, 6375 (2001).
39. D. Marenduzzo, A. Maritan, E. Orlandini, F. Seno, and A. Trovato, e-print arXiv:0807.3236, 2008.
40. I. Rouzina and V. A. Bloomfield, Biophys. J. 80, 882 (2001). 0006-3495
41. A. Hanke, M. G. Ochoa, and R. Metzler, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.100.018106 100, 018106 (2008).
42. J. Rudnick and T. Kuriabova, Phys. Rev. E 1063-651X 10.1103/PhysRevE.77. 051903 77, 051903 (2008).
43. S. J. Rahi, M. P. Hertzberg, and M. Kardar, Phys. Rev. E 1063-651X 10.1103/PhysRevE.78.051910 78, 051910 (2008).
44. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.63.1195 63, 1195 (1989).