Coarse-grained modeling of DNA curvature

Journal of Chemical Physics

Volumn 141, Issue 16, 2014, Pages

  Freeman, Gordon S ^a   Hinckley, Daniel M ^a   Lequieu, Joshua P ^b   Whitmer, Jonathan K ^c   De Pablo, Juan J ^b,c  

^a University of Wisconsin Madison   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOCHEMISTRY; PROTEINS;

COARSE GRAINED MODELS; INTRINSIC CURVATURE; LOCAL CURVATURE; LOCAL FLEXIBILITY; LOCAL STRUCTURE; PERSISTENCE LENGTH; PROTEIN BINDING PROPERTIES; SEQUENCE-DEPENDENT;

DNA;

DNA;

BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; DNA DENATURATION; GENETICS; NUCLEOTIDE SEQUENCE; TRANSITION TEMPERATURE;

BASE PAIRING; BASE SEQUENCE; DNA; MODELS, MOLECULAR; NUCLEIC ACID DENATURATION; TRANSITION TEMPERATURE;

EID: 84908464352     PISSN: 00219606     EISSN: 10897690     Source Type: Journal    
DOI: 10.1063/1.4897649     Document Type: Article

References (41)

1. J. Moreno-Razo, E. Sambriski, N. Abbott, J. Hernández-Ortiz, and J. de Pablo, Nature (London) 485, 86 (2012). 10.1038/nature11084
2. F. A. Detcheverry, H. Kang, K. C. Daoulas, M. Müller, P. F. Nealey, and J. J. de Pablo, Macromolecules 41, 4989 (2008). 10.1021/ma702514v
3. V. Tozzini, Curr. Opin. Struc. Biol. 15, 144 (2005). 10.1016/j.sbi.2005.02.005
4. T. A. Knotts, N. Rathore, D. C. Schwartz, and J. J. de Pablo, J. Chem. Phys. 126, 084901 (2007). 10.1063/1.2431804
5. D. M. Hinckley, J. S. Lequieu, and J. J. de Pablo, J. Chem. Phys. 141, 035102 (2014). 10.1063/1.4886336
6. F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, and A. A. Louis, J. Chem. Phys. 138, 085101 (2013). 10.1063/1.4792252
7. A. Zeida, M. R. Machado, P. D. Dans, and S. Pantano, Phys. Rev. E 86, 021903 (2012). 10.1103/PhysRevE.86.021903
8. P. D. Dans, A. Zeida, M. R. Machado, and S. Pantano, J. Chem. Theory Comput. 6, 1711 (2010). 10.1021/ct900653p
9. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011). 10.1063/1.3552946
10. L. E. Edens, J. A. Brozik, and D. J. Keller, J. Phys. Chem. B 116, 14735 (2012). 10.1021/jp3009095
11. Y. He, M. Maciejczyk, S. Ołdziej, H. A. Scheraga, and A. Liwo, Phys. Rev. Lett. 110, 098101 (2013). 10.1103/PhysRevLett.110.098101
12. D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013). 10.1063/1.4822042
13. W. K. Olson, A. A. Gorin, X.-J. Lu, L. M. Hock, and V. B. Zhurkin, Proc. Natl. Acad. Sci. U.S.A. 95, 11163 (1998). 10.1073/pnas.95.19.11163
14. R. Lavery, K. Zakrzewska, D. Beveridge, T. C. Bishop, D. A. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J. H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, and S. Jiri, Nucl. Acids Res. 38, 299 (2010). 10.1093/nar/gkp834
15. S. Arnott, P. J. Campbell Smith, and R. Chandrasekaran, Handbook of Biochemistry and Molecular Biology (CRC, 1976), Vol. 2, p. 411.
16. P. De Santis and A. Scipioni, Phys. Life Rev. 10, 41 (2013). 10.1016/j.plrev.2013.01.004
17. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo, Biophys. J. 96, 1675 (2009). 10.1016/j.bpj.2008.09.061
18. S. Geggier and A. Vologodskii, Proc. Natl. Acad. Sci. U.S.A. 107, 15421 (2010). 10.1073/pnas.1004809107
19. A. Laio and F. L. Gervasio, Rep. Prog. Phys. 71, 126601 (2008). 10.1088/0034-4885/71/12/126601
20. P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello, J. Phys. Chem. B 110, 3533 (2006). 10.1021/jp054359r
21. P. Protozanova, E. Yakovchuk, and M. D. Frank-Kamenetskii, J. Mol. Biol. 342, 775 (2004). 10.1016/j.jmb.2004.07.075
22. R. Owczarzy, Y. You, B. G. Moreira, J. A. Manthey, L. Huang, M. A. Behlke, and J. A. Walder, Biochemistry 43, 3537 (2004). 10.1021/bi034621r
23. P. C. Kahn, Comput. Chem. 13, 185 (1989). 10.1016/0097-8485(89)85005-3
24. B. Tinland, A. Pluen, J. Sturm, and G. Weill, Macromolecules 30, 5763 (1997). 10.1021/ma970381+
25. E. Segal, Y. Fondufe-Mittendorf, L. Chen, A. Thåström, Y. Field, I. K. Moore, J.-P. Z. Wang, and J. Widom, Nature (London) 442, 772 (2006). 10.1038/nature04979
26. S. M. West, R. Rohs, R. S. Mann, and B. Honig, J. Biomol. Struct. Dyn. 27, 861 (2010). 10.1080/07391102.2010.10508587
27. R. Rohs, S. M. West, A. Sosinsky, P. Liu, R. S. Mann, and B. Honig, Nature (London) 461, 1248 (2009). 10.1038/nature08473
28. A. Scipioni, S. Pisano, C. Anselmi, M. Savino, and P. De Santis, Biophys. Chem. 107, 7 (2004). 10.1016/S0301-4622(03)00214-X
29. J. P. Peters and L. J. Maher, Q. Rev. Biophys. 43, 23 (2010). 10.1017/S0033583510000077
30. A. V. Morozov, K. Fortney, D. A. Gaykalova, V. M. Studitsky, J. Widom, and E. D. Siggia, Nucl. Acids Res. 37, 4707 (2009). 10.1093/nar/gkp475
31. W. K. Olson, A. V. Colasanti, Y. Li, W. Ge, G. Zheng, and V. B. Zhurkin, Computational Studies of RNA and DNA (Springer, 2006), pp. 235-257. 10.1007/978-1-4020-4851-3-9
32. P. De Santis, A. Palleschi, M. Savino, and A. Scipioni, Biochemistry 29, 9269 (1990). 10.1021/bi00491a023
33. X.-J. Lu and W. K. Olson, Nucl. Acids Res. 31, 5108 (2003). 10.1093/nar/gkg680
34. M. A. El Hassan and C. R. Calladine, J. Mol. Biol. 251, 648 (1995). 10.1006/jmbi.1995.0462
35. P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, and A. A. Louis, J. Chem. Phys. 137, 135101 (2012). 10.1063/1.4754132
36. S. Lindemose, P. E. Nielsen, M. Hansen, and N. E. Møllegaard, Nucl. Acids Res. 39, 6269 (2011). 10.1093/nar/gkr204
37. E. P. Bishop, R. Rohs, S. C. J. Parker, S. M. West, P. Liu, R. S. Mann, B. Honig, and T. D. Tullius, ACS Chem. Biol. 6, 1314 (2011). 10.1021/cb200155t
38. G. S. Freeman, J. P. Lequieu, D. M. Hinckley, J. K. Whitmer, and J. J. de Pablo, Phys. Rev. Lett. 113, 168101 (2014). 10.1103/PhysRevLett.113.168101
39. S. Plimpton, J. Comput. Phys. 117, 1 (1995). 10.1006/jcph.1995.1039
40. See lammps.sandia.gov in order to download LAMMPS.
41. See https://uchic.ag/3spn2 for the USER-3SPN2 package that enables simulation of 3SPN.2C in LAMMPS.