Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

Physical Review Letters

Volumn 110, Issue 9, 2013, Pages

  He, Yi ^a   MacIejczyk, MacIej ^a,b   Ołdziej, Stanisław ^a,c   Scheraga, Harold A ^a   Liwo, Adam ^c  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF WARMIA AND MAZURY IN OLSZTYN   (Poland)

^c UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CHAIN CONNECTIVITY; COARSE GRAINED MODELS; DOUBLE HELIX; DOUBLE-HELICAL STRUCTURES; EXCLUDED-VOLUME INTERACTIONS; LOCAL INTERACTIONS; MEAN-FIELD; MEAN-FIELD INTERACTIONS; MULTIPOLE-MULTIPOLE INTERACTIONS; PRINCIPAL FACTORS; PROTEIN MODELS; REGULAR STRUCTURE; RNA MOLECULES;

RNA;

BIOMOLECULES;

DNA; RNA;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; THERMODYNAMICS;

DNA; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

EID: 84874539246     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.110.098101     Document Type: Article

References (26)

1. J. D. Watson and H. C. Crick, Nature (London) 171, 737 (1953). NATUAS 0028-0836 10.1038/171737a0
2. J. Bath and A. J. Turberfield, Nat. Nanotechnol. 2, 275 (2007). NNAABX 1748-3387 10.1038/nnano.2007.104 (Pubitemid 46882966)
3. D. A. Brant and P. J. Flory, J. Am. Chem. Soc. 87, 663 (1965). JACSAT 0002-7863 10.1021/ja01081a054
4. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989). PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755
5. W. K. Olson, Curr. Opin. Struct. Biol. 6, 242 (1996). COSBEF 0959-440X 10.1016/S0959-440X(96)80082-0 (Pubitemid 26128830)
6. C. Hyeon and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. 102, 6789 (2005). PNASA6 0027-8424 10.1073/pnas.0408314102 (Pubitemid 40675394)
7. T. Knotts IV, N. Rathore, D. C. Schwartz, and J. J. de Pablo, J. Chem. Phys. 126, 084901 (2007). JCPSA6 0021-9606 10.1063/1.2431804 (Pubitemid 46357459)
8. K. Voltz, J. Trylska, V. Tozzini, V. Kurkal-Siebert, J. Langowski, and J. Smith, J. Comput. Chem. 29, 1429 (2008). JCCHDD 0192-8651 10.1002/jcc.20902 (Pubitemid 351757766)
9. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 104, 178101 (2010). PRLTAO 0031-9007 10.1103/PhysRevLett.104.178101
10. M. Maciejczyk, A. Spasic, A. Liwo, and H. A. Scheraga, J. Comput. Chem. 31, 1644 (2010). JCCHDD 0192-8651 10.1002/jcc.21448
11. M. Zuker, Nucleic Acids Res. 31, 3406 (2003). NARHAD 1362-4962 10.1093/nar/gkg595 (Pubitemid 37442169)
12. N. R. Markham and M. Zuker, in Bioinformatics, edited by, J. M. Keith, Methods in Molecular Biology Vol. 453 (Humana Press, Totowa, NJ, 2008), Chap., pp. 3-31.
13. J. SantaLucia and D. Hicks, Annu. Rev. Biophys. Biomol. Struct. 33, 415 (2004). ABBSE4 1056-8700 10.1146/annurev.biophys.32.110601.141800 (Pubitemid 38829966)
14. A. Liwo, M. R. Pincus, R. J. Wawak, S. Rackovsky, and H. A. Scheraga, Protein Sci. 2, 1715 (1993). PRCIEI 0961-8368 10.1002/pro.5560021016
15. A. Liwo, C. Czaplewski, J. Pillardy, and H. A. Scheraga, J. Chem. Phys. 115, 2323 (2001). JCPSA6 0021-9606 10.1063/1.1383989 (Pubitemid 32742790)
16. A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Ołdziej, K. Wachucik, and H. A. Scheraga, J. Phys. Chem. B 111, 260 (2007). JPCBFK 1520-6106 10.1021/jp065380a (Pubitemid 46277990)
17. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.110.098101 for the detailed description of the NARES-2P energy function (Sec. S1), its current parameterization (Sec. S2), description of replica-exchange simulations (Sec. S3), results of the calculations of thermodynamic properties of the melting transition of the 18 selected DNA molecules and their comparison with the experimental values (Sec. S4), results of the simulation of bubble formation (Sec. S5), and essential-dynamics analysis of all-atom and NARES-2P canonical molecular dynamics trajectories (Sec. S6).
18. A. Liwo, M. Khalili, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 102, 2362 (2005). PNASA6 0027-8424 10.1073/pnas.0408885102 (Pubitemid 40279381)
19. C. Czaplewski, S. Kalinowski, A. Liwo, and H. A. Scheraga, J. Chem. Theory Comput. 5, 627 (2009). 1549-9618 10.1021/ct800397z
20. C. Mandal, N. R. Kallenbach, and S. W. Englander, J. Mol. Biol. 135, 391 (1979). JMOBAK 0022-2836 10.1016/0022-2836(79)90443-1 (Pubitemid 10173569)
21. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003). PRLTAO 0031-9007 10.1103/PhysRevLett.90.138101
22. D. Poland and H. A. Scheraga, J. Chem. Phys. 45, 1464 (1966). JCPSA6 0021-9606 10.1063/1.1727786
23. Y. Zeng, A. Montrichok, and G. Zocchi, J. Mol. Biol. 339, 67 (2004). JMOBAK 0022-2836 10.1016/j.jmb.2004.02.072 (Pubitemid 38569690)
24. S. Cuesta-Lopez, H. Menoni, D. Angelov, and M. Peyrard, Nucleic Acids Res. 39, 5276 (2011). NARHAD 0305-1048 10.1093/nar/gkr096
25. E. Giudice and R. Lavery, Acc. Chem. Res. 35, 350 (2002). ACHRE4 0001-4842 10.1021/ar010023y
26. A. Liwo, S. Ołdziej, C. Czaplewski, D. S. Kleinerman, P. Blood, and H. A. Scheraga, J. Chem. Theory Comput. 6, 890 (2010). 1549-9618 10.1021/ct9004068