Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Journal of Physics Condensed Matter

Volumn 21, Issue 3, 2009, Pages

  Peyrard, M ^a   Cuesta Lopez S ^a   Angelov, D ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE ENCODING; MELTING;

CHARACTERISTIC SEQUENCE; DNA MOLECULES; GENETIC CODE; LONG SEQUENCES; MESOSCOPIC MODELING; NEW EXPERIMENTAL METHOD; NON-LOCAL EFFECT; THEORETICAL STUDY;

DNA SEQUENCES;

EID: 63649093021     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/21/3/034103     Document Type: Article

References (41)

1. Wartell R M and Benight A S 1985 Phys. Rep. 126 67-107
2. Wada A, Yabuki S and Husimi Y 1980 CRC Crit. Rev. Biochem. 9 87-144
3. Essevaz-Roulet B, Bockelmann U and Heslot F 1997 Proc. Natl Acad. Sci. USA 94 11935-40
4. Leroy J L, Kochoyan M, Huynh-Dinh T and Guéron M 1988 J. Mol. Biol. 200 223-8
5. Montrichok A, Gruner G and Zocchi G 2003 Europhys. Lett. 62 452-8
6. Zeng Y, Montrichok A and Zocchi G 2004 J. Mol. Biol. 339 67-75
7. Brauns E B, Murphy C J and Berg M A 1998 J. Am. Chem. Soc. 120 2449-56
8. Altan-Bonnet G, Libchaber A and Krichevsky O 2003 Phys. Rev. Lett. 90 138101
9. Douki T, Ravanat J-L, Angelov D, Wagner J R and Cadet J 2004 Top. Curr. Chem. 236 1-25
10. Angelov D, Beylot B and Spassky A 2005 Biophys. J. 88 2766-78
11. Spassky A and Angelov D 1997 Biochemistry 36 6571-6
12. Erfurth S C and Peticolas W L 1975 Biopolymers 14 247-64
13. Chan S S, Breslauer K J, Hogan M E, Kessler D J, Austin R H, Ojemann J, Passner J M and Wiles N C 1990 Biochemistry 29 6161-71
14. Chan S S, Breslauer K J, Austin R H and Hogan M E 1993 Biochemistry 32 11776-84
15. Movileanu L, Benevides J M and Thomas G J Jr 2002 Nucl. Acid Res. 30 3767-77
16. Zimm B H 1960 J. Chem. Phys. 33 1349-56
17. Poland D and Scheraga H A 1966 J. Chem. Phys. 45 1456-63
18. Poland D and Scheraga H A 1966 J. Chem. Phys. 45 1464-9
19. Kafri Y, Mukamel D and Peliti L 2000 Phys. Rev. Lett. 85 4988-91
20. Fixman M and Freire J J 1977 Biopolymers 16 2693-704
21. Yeramian E 2000 Gene 255 139-50
22. Blossey R and Carlon E 2003 Phys. Rev. E 68 061911
23. Dimitrov R A and Zuker M 2004 Biophys. J. 87 215-26 http://www.bioinfo. rpi.edu/applications/hybrid/hybrid2.php
24. Carlon E, Dkhissi A, Malki M L and Blossey R 2007 Phys. Rev. E 76 051916
25. SantaLucia J, Allawi H T and Ananda Seneviratne P 1996 Biochemistry 35 3555-62
26. Peyrard M 2004 Nonlinearity 17 R1-40
27. Peyrard M 2008 Nonlinearity 21 T91-100
28. Peyrard M and Bishop A R 1989 Phys. Rev. Lett. 62 2755-8
29. Drukker K, Wu G and Schatz G C 2001 J. Chem. Phys. 114 579-90
30. Weber G 2006 Europhys. Lett. 73 806-11
31. Theodorakopoulos N, Dauxois T and Peyrard M 2000 Phys. Rev. Lett. 85 6-9
32. Dauxois T, Peyrard M and Bishop A R 1993 Phys. Rev. E 47 R44-7
33. Giudice E, Vrnai P and Lavery R 2003 Nucleic Acids Res. 31 1434-43
34. van Erp T S, Cuesta-López S and Peyrard M 2006 Eur. Phys. J. E 20 421-34
35. Campa A and Giansanti A 1998 Phys. Rev. E 58 3585-8
36. Gotoh O and Tagashira Y 1981 Biopolymers 20 1033-42
37. Saenger W 1984 Principles of Nucleic Acid Structure (Berlin: Springer)
38. Cuesta-López S, Wildes A, Theodorakopoulos N and Peyrard M 2008 unpublished
39. Errami J, Peyrard M and Theodorakopoulos N 2007 Eur. Phys. J. E 23 397-411
40. Dauxois T, Peyrard M and Bishop A R 1993 Phys. Rev. E 47 684-95
41. Cuesta-López S, Angelov D and Peyrard M 2008 unpublished