Mechanical transition in a highly stretched and torsionally constrained DNA

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

Volumn 89, Issue 2, 2014, Pages

  Strzelecki, Janusz ^a   Peplowski, Lukasz ^a   Lenartowski, Robert ^b   Nowak, Wieslaw ^a   Balter, Aleksander ^a  

^a NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^b Institute of Ecology and Environmental Protection   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE HELIX; DOUBLE STRANDED DNA; FORCE SPECTRA; FORCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATIONS; ROTATIONAL FREEDOM;

ATOMIC FORCE MICROSCOPY; MOLECULAR DYNAMICS; MOLECULES;

DNA;

DNA;

CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; MATERIALS TESTING; MECHANICAL STRESS; TORQUE; ULTRASTRUCTURE; YOUNG MODULUS;

COMPUTER SIMULATION; DNA; ELASTIC MODULUS; MATERIALS TESTING; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; STRESS, MECHANICAL; TORQUE;

EID: 84897756579     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.89.020701     Document Type: Article

References (28)

1. A. V. Pinheiro, D. Han, W. M. Shih, and H. Yan, Nat. Nanotechnol. 6, 763 (2011). 10.1038/nnano.2011.187
2. S. B. Smith, L. Finzi, and C. Bustamante, Science 258, 1122 (1992). SCIEAS 0036-8075 10.1126/science.1439819
3. C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, Curr. Opin. Struct. Biol. 10, 279 (2000). COSBEF 0959-440X 10.1016/S0959-440X(00)00085-3 (Pubitemid 30333096)
4. C. Bustamante, Z. Bryant, and S. B. Smith, Nature (London) 421, 423 (2003). 10.1038/nature01405 (Pubitemid 36157948)
5. J. F. Marko and S. Cocco, Phys. World 16, 37 (2003).
6. C. Prévost, M. Takahashi, and R. Lavery, Chem. Phys. Chem. 10, 1399 (2009). CPCHFT 1439-4235 10.1002/cphc.200900253
7. S. B. Smith, Y. Cui, and C. Bustamante, Science 271, 795 (1996). SCIEAS 0036-8075 10.1126/science.271.5250.795
8. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J. L. Viovy, D. Chatenay, and F. Caron, Science 271, 792 (1996). SCIEAS 0036-8075 10.1126/science.271.5250. 792
9. N. Bosaeus, A. H. El-Sagheer, T. Brown, S. B. Smith, B. Åkerman, C. Bustamante, and B. Nordén, Proc. Natl. Acad. Sci. U.S.A. 109, 15179 (2012). 10.1073/pnas.1213172109
10. X. Zhang, H. Chen, S. Le, I. Rouzina, P. S. Doyle, and J. Yan, Proc. Natl. Acad. Sci. U.S.A. 110, 3865 (2013). 10.1073/pnas.1213740110
11. D. H. Paik and T. T. Perkins, J. Am. Chem. Soc. 133, 3219 (2011). 10.1021/ja108952v
12. J. F. Leger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J. F. Marko, Phys. Rev. Lett. 83, 1066 (1999). PRLTAO 0031-9007 10.1103/PhysRevLett.83.1066
13. M. Rief, H. Clausen-Schaumann, and H. E. Gaub, Nat. Struct. Biol. 6, 346 (1999). NSBIEW 1072-8368 10.1038/7582 (Pubitemid 29166483)
14. H. Clausen-Schaumann, M. Rief, C. Tolksdorf, and H. E. Gaub, Biophys. J. 78, 1997 (2000). BIOJAU 0006-3495 10.1016/S0006-3495(00)76747-6
15. C. P. Calderon, W. H. Chen, K. J. Lin, N. C. Harris, and C. H. Kiang, J. Phys.: Condens. Matter 21, 034114 (2009). 10.1088/0953-8984/21/3/034114
16. T. Hugel, M. Rief, M. Seitz, H. E. Gaub, and R. R. Netz, Phys. Rev. Lett. 94, 048301 (2005). PRLTAO 0031-9007 10.1103/PhysRevLett.94.048301 (Pubitemid 40607260)
17. A. A. Guerrero, M. C. Gamero, V. Trachana, A. Fütterer, C. Pacios-Bras, N. P. Díaz-Concha, J. C. Cigudosa, C. Martínez-A, and K. H. M. Van Wely, Proc. Natl. Acad. Sci. U.S.A. 107, 4159 (2010). 10.1073/pnas.0912143106
18. N. J. Ganem and D. Pellman, J. Cell Biol. 199, 871 (2012). JCLBA3 0021-9525 10.1083/jcb.201210040
19. W. Hu, PloS One 7, e51905 (2012). 10.1371/journal.pone.0051905
20. J. C. Phillips, J. Comput. Chem. 26, 1781 (2005). JCCHDD 0192-8651 10.1002/jcc.20289 (Pubitemid 43078511)
21. A. D. MacKerell, Jr., J. Phys. Chem. B 102, 3586 (1998). JPCBFK 1520-6106 10.1021/jp973084f
22. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevE.89.020701 for the AFM force spectroscopy experiment procedure and SMD simulation details.
23. M. Rabbi and P. E. Marszalek, Cold Spring Harbor Protoc. 2007, pdb. prot4900 (2007). 10.1101/pdb.prot4900
24. J. Allemand, D. Bensimon, R. Lavery, and V. Croquette, Proc. Natl. Acad. Sci. U.S.A. 95, 14152 (1998). 10.1073/pnas.95.24.14152 (Pubitemid 28549336)
25. A. Balaeff, S. L. Craig, and D. N. Beratan, J. Phys. Chem. A 115, 9377 (2011). 10.1021/jp110871g
26. M. Maaloum, A. F. Beker, and P. Muller, Phys. Rev. E 83, 031903 (2011). PLEEE8 1063-651X 10.1103/PhysRevE.83.031903
27. J. Van Mameren, P. Gross, G. Farge, P. Hooijman, M. Modesti, M. Falkenberg, G. J. L. Wuite, and E. J. G. Peterman, Proc. Natl. Acad. Sci. U.S.A. 106, 18231 (2009). 10.1073/pnas.0904322106
28. R. Perez-Jimenez, A. P. Wiita, D. Rodriguez-Larrea, P. Kosuri, J. A. Gavira, J. M. Sanchez-Ruiz, and J. M. Fernandez, J. Biol. Chem. 283, 27121 (2008). JBCHA3 0021-9258 10.1074/jbc.M803746200