Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

Journal of Physical Chemistry B

Volumn 114, Issue 2, 2010, Pages 1191-1203

  Svozil, Daniel ^a   Hobza, Pavel ^b,c   Šponer, Jiří ^d  

^a INSTITUTE OF CHEMICAL TECHNOLOGY   (Czech Republic)

^b INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^c PALACKÝ UNIVERSITY   (Czech Republic)

^d INSTITUTE OF BIOPHYSICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMOBILE EXHIBITIONS; CHEMICAL STABILITY; DIFFRACTION; GASES; GENES; GEOMETRY; HYDROCARBONS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; QUANTUM CHEMISTRY; RNA; SEPARATION; SYSTEM STABILITY; VAN DER WAALS FORCES;

AB INITIO METHOD; BALANCE OF FORCE; BASE PAIRS; BASE STACKING; DINUCLEOTIDES; DNA DUPLEXES; DOUBLE HELIX; ENERGY DIFFERENCES; FIBER DIFFRACTION; GASPHASE; INTERACTION ENERGIES; MD SIMULATION; METHYL GROUP; MOLECULAR DYNAMICS SIMULATIONS; NEAREST-NEIGHBORS; QUANTUM-CHEMICAL CALCULATION; STACKING ENERGY; STACKING INTERACTION; VAN DER WAALS EFFECT;

DNA;

EID: 75649121122     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp910788e     Document Type: Article

References (127)

1. Arnott, S.; Hukins, D. W. L. Biochem. Biophys. Res. Commun. 1972, 47, 1504-1511.
2. Nir, E.; Grace, L.; Brauer, B.; de Vries, M. S. J. Am. Chem. Soc. 1999, 121, 4896-4897.
3. Nir, E.; Kleinermanns, K.; de Vries, M. S. Nature 2000, 408, 949-951.
4. Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. Phys. Chem. Chem. Phys. 2002, 4, 740-750.
5. Nir, E.; Muller, M.; Grace, L. I.; de Vries, M. S. Chem. Phys. Lett. 2002, 355, 59-64.
6. Plutzer, C.; Hunig, I.; Kleinermanns, K.; Nir, E.; de Vries, M. S. Chem. Phys. Chem. 2003, 4, 838-842.
7. Hobza, P.; Sponer, J. J. Am. Chem. Soc. 2002, 124, 11802-11808.
8. Jurecka, P.; Hobza, P. J. Am. Chem. Soc. 2003, 125, 15608-15613.
9. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J. Am. Chem. Soc. 2002, 124, 104-112.
10. Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. J. Am. Chem. Soc. 2002, 124, 10887-10893.
11. Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Abstr. Pap. Am. Chem. Soc. 2003, 225, U476.
12. Sinnokrot, M. O.; Sherrill, C. D. J. Phys. Chem. A 2004, 108, 10200-10207.
13. Tauer, T. P.; Sherrill, C. D. J. Phys. Chem. A 2005, 109, 10475-10478.
14. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 4209-4212.
15. Manojkumar, T. K.; Kim, D.; Kim, K. S. J. Chem. Phys. 2005, 122.
16. Piacenza, M.; Grimme, S. J. Am. Chem. Soc. 2005, 127, 14841-14848.
17. Tsuzuki, S.; Uchimaru, T.; Mikami, M. J. Phys. Chem. A 2006, 110, 2027-2033.
18. Podeszwa, R.; Bukowski, R.; Szalewicz, K. J. Phys. Chem. A. 2006, 110, 10345-10354.
19. DiStasio, R. A.; von Helden, G.; Steele, R. P.; Head-Gordon, M. Chem. Phys. Lett. 2007, 437, 277-283.
20. Lee, E. C.; Kim, D.; Jurecka, P.; Tarakeshwar, P.; Hobza, P.; Kim, K. S. J. Phys. Chem. A 2007, 111, 3446-3457.
21. Takatani, T.; Sherrill, C. D. Phys. Chem. Chem. Phys. 2007, 9, 6106-6114.
22. Pitonak, M.; Neogrady, P.; Rezac, J.; Jurecka, P.; Urban, M.; Hobza, P. J. Chem. Theory Comput. 2008, 4, 1829-1834.
23. Cooper, V. R.; Thonhauser, T.; Puzder, A.; Schroder, E.; Lundqvist, B. I.; Langreth, D. C. J. Am. Chem. Soc. 2008, 130, 1304-1308.
24. Li, S.; Cooper, V. R.; Thonhauser, T.; Lundqvist, B. I.; Langreth, D. C. J. Phys. Chem. B 2009, 113, 11166-11172.
25. Cysewski, P. New J. Chem. 2009, 33, 1909-1917.
26. Morgado, C. A.; Jurecka, P.; Svozil, D.; Hobza, P.; Sponer, J. J. Chem. Theory Comput. 2009, 5, 1524-1544.
27. Sherrill, C. D.; Takatani, T.; Hohenstein, E. G. J. Phys. Chem. A 2009, 113, 10146-10159.
28. Sherrill, C. D.; Sumpter, B. G.; Sinnokrot, M. O.; Marshall, M. S.; Hohenstein, E. G.; Walker, R. C.; Gould, I. R. J. Comput. Chem. 2009, 30, 2187-2193.
29. Grafenstein, J.; Cremer, D. J. Chem. Phys. 2009, 130.
30. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 1965-1974.
31. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590-5596.
32. Sponer, J.; Burda, J. V.; Sabat, M.; Leszczynski, J.; Hobza, P. J. Phys. Chem. A 1998, 102, 5951-5957.
33. Sponer, J.; Sponer, J. E.; Gorb, L.; Leszczynski, J.; Lippert, B. J. Phys. Chem. A 1999, 103, 11406-11413.
34. Spackova, N.; Cheatham, T. E.; Ryjacek, F.; Lankas, F.; van Meervelt, L.; Hobza, P.; Sponer, J. J. Am. Chem. Soc. 2003, 125, 1759-1769.
35. Reha, D.; Kabelac, M.; Ryjacek, F.; Sponer, J.; Sponer, J. E.; Elstner, M.; Suhai, S.; Hobza, P. J. Am. Chem. Soc. 2002, 124, 3366-3376.
36. Jurecka, P.; Cerny, J.; Hobza, P.; Salahub, D. R. J. Comput. Chem. 2007, 28, 555-569.
37. Cerny, J.; Jurecka, P.; Hobza, P.; Valdes, H. J. Phys. Chem. A 2007, 111, 1146-1154.
38. SantaLucia, J.; Hicks, D. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 415-440.
39. Xia, T. B.; SantaLucia, J.; Burkard, M. E.; Kierzek, R.; Schroeder, S. J.; Jiao, X. Q.; Cox, C.; Turner, D. H. Biochemistry 1998, 37, 14719-14735.
40. Alhambra, C.; Luque, F. J.; Gago, F.; Orozco, M. J. Phys. Chem. B 1997, 101, 3846-3853.
41. Bansal, M.; Bhattacharyya, D.; Ravi, B. Comput. Appl. BioSci. 1995, 11, 281-287.
42. Lu, X. J.; Olson, W. K. Nucleic Acids Res. 2003, 31, 5108-5121.
43. Macke, T.; Case, D. A. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids; Leontis, N. B., SantaLucia, J., Eds.; American Chemical Society: Washington, DC, 1998; pp 379-393.
44. Schneider, B.; Neidle, S.; Berman, H. M. Biopolymers 1997, 42, 113-124.
45. Gorin, A. A.; Zhurkin, V. B.; Olson, W. K. J. Mol. Biol. 1995, 247, 34-48.
46. ElHassan, M. A.; Calladine, C. R. Phil. Trans. R. Soc. London Ser. A-Math. Phys. Ens. Sci. 1997, 355, 43-100.
47. Cysewski, P. J. Mol. Struct. (THEOCHEM) 2008, 865, 36-43.
48. Cysewski, P.; Czyznikowska, Z.; Zalesny, R.; Czelen, P. Phys. Chem. Chem. Phys. 2008, 10, 2665-2672.
49. Czyznikowska, Z. J. Mol. Struct. (THEOCHEM) 2009, 895, 161-167.
50. Sponer, J.; Florian, J.; Ng, H. L.; Sponer, J. E.; Spackova, N. Nucleic Acids Res. 2000, 28, 4893-4902.
51. Sponer, J.; Gabb, H. A.; Leszczynski, J.; Hobza, P. Biophys. J. 1997, 73, 76-87.
52. Sponer, J.; Kypr, J. J. Biomol. Struct. Dyn. 1993, 11, 277-292.
53. Svozil, D.; Kalina, J.; Omelka, M.; Schneider, B. Nucleic Acids Res. 2008, 36, 3690-3706.
54. Olson, W. K.; et al. J. Mol. Biol. 2001, 313, 229-237.
55. Fiethen, A.; Jansen, G.; Hesselmann, A.; Schotz, M. J. Am. Chem. Soc. 2008, 130, 1802.
56. Sponer, J.; Riley, K. E.; Hobza, P. Phys. Chem. Chem. Phys. 2008, 10, 2595-2610.
57. Sponer, J.; Kypr, J. Int. J. Biol. Macromol. 1994, 16, 3-6.
58. Sponer, J.; Hobza, P. J. Am. Chem. Soc. 1994, 116, 709-714.
59. Sponer, J.; Jurecka, P.; Marchan, I.; Luque, F. J.; Orozco, M.; Hobza, P. Chems-Eur. J. 2006, 12, 2854-2865.
60. Cysewski, P.; Czyznikowska-Balcerak, Z. J. Mol. Struct. (THEOCHEM) 2005, 757, 29-36.
61. Langner, K. M.; Sokalski, W. A.; Leszczynski, J. J. Chem. Phys. 2007, 127.
62. Hill, J. G.; Platts, J. A. Phys. Chem. Chem. Phys. 2008, 10, 2785-2791.
63. Sponer, J.; Kypr, J. J. Mol. Biol. 1991, 221, 761-764.
64. Dockbregeon, A. C.; Chevrier, B.; Podjarny, A.; Johnson, J.; Debear, J. S.; Gough, G. R.; Gilham, P. T.; Moras, D. J. Mol. Biol. 1989, 209, 459-474.
65. Beveridge, D. L.; McConnell, K. J. Curr. Opin. Struct. Biol. 2000, 10, 182-196.
66. Giudice, E.; Lavery, R. Acc. Chem. Res. 2002, 35, 350-357.
67. Cheatham, T. E. Curr. Opin. Struct. Biol. 2004, 14, 360-367.
68. Auffinger, P.; Westhof, E. Curr. Opin. Struct. Biol. 1998, 8, 227-236.
69. Orozco, M.; Perez, A.; Noy, A.; Luque, F. J. Chem. Soc. Rev. 2003, 32, 350-364.
70. McDowell, S. E.; Spackova, N.; Sponer, J.; Walter, N. G. Biopolymers 2007, 85, 169-184.
71. Olson, W. K.; Colasanti, A.; Li, Y.; Zheng, W. G.; Zhurkin, V. B. DNA simulation benchmarks as revealed by X-ray structures. In Computational studies ofRNA and DNA, Sponer, J., Lankas, F., Eds.; Springer: Dordrecht, The Netherlands, 2006; pp 235-257.
72. Beveridge, D. L.; et al. Biophys. J. 2004, 87, 3799-3813.
73. Barone, F.; Lankas, F.; Spackova, N.; Sponer, J.; Karran, P.; Bignami, M.; Mazzei, F. Biophys. Chem. 2005, 118, 31-41.
74. Varnai, P.; Zakrzewska, K. Nucleic Acids Res. 2004, 32, 4269-4280.
75. Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
76. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829.
77. Lankas, F.; Sponer, J.; Langowski, J.; Cheatham, T. E. Biophys. J. 2003, 85, 2872-2883.
78. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668-1688.
79. Perez, A.; Lankas, F.; Luque, F. J.; Orozco, M. Nucleic Acids Res. 2008, 36, 2379-2394.
80. Dixit, S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E.; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Biophys. J. 2005, 89, 3721-3740.
81. Dixit, S. B.; Beveridge, D. L. Bioinformatics 2006, 22, 1007-1009.
82. Reblova, K.; Lankas, F.; Razga, F.; Krasovska, M. V.; Koca, J.; Sponer, J. Biopolymers 2006, 82, 504-520.
83. Schneider, B.; Moravek, Z.; Berman, H. M. Nucleic Acids Res. 2004, 32, 1666-1677.
84. Moody, E. M.; Bevilacqua, P. C. J. Am. Chem. Soc. 2003, 125, 2032-2033.
85. Mignon, P.; Loverix, S.; Steyaert, J.; Geerlings, P. Nucleic Acids Res. 2005, 33, 1779-1789.
86. Vanommeslaeghe, K.; Mignon, P.; Loverix, S.; Tourwe, D.; Geerlings, P. J. Chem. Theory Comput. 2006, 2, 1444-1452.
87. Gil, A.; Branchadell, V.; Bertran, J.; Oliva, A. J. Phys. Chem. B 2009, 113, 4907-4914.
88. Antony, J.; Bruske, B.; Grimme, S. Phys. Chem. Chem. Phys. 2009, 11, 8440-8447.
89. Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Phys. Chem. Chem. Phys. 2006, 8, 1985-1993.
90. Kubar, T.; Jurecka, P.; Cerny, J.; Rezac, J.; Otyepka, M.; Valdes, H.; Hobza, P. J. Phys. Chem. A 2007, 111, 5642-5647.
91. Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C. Chem. Phys. Lett. 1989, 162, 165-169.
92. Eichkorn, K.; Treutler, O.; Ohm, H.; Haser, M.; Ahlrichs, R. Chem. Phys. Lett. 1995, 240, 283-289.
93. Baerends, E. J.; Ellis, D. E.; Ros, P. Chem. Phys. 1973, 2, 41-51.
94. Whitten, J. L. J. Chem. Phys. 1973, 58, 4496-1501.
95. Dunlap, B. I.; Connolly, J. W. D.; Sabin, J. R. J. Chem. Phys. 1979, 71, 3396-3402.
96. Halkier, A.; Helgaker, T.; Jorgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Chem. Phys. Lett. 1998, 286, 243-252.
97. Molpro 2006.1, A Package of Ab Initio Programs, 2006.
98. Sponer, J.; Hobza, P. Collect. Czech. Chem. Commun. 2003, 68, 2231-2282.
99. Leininger, M. L.; Nielsen, I. M. B.; Colvin, M. E.; Janssen, C. L. J. Phys. Chem. A 2002, 106, 3850-3854.
100. Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247-3276.
101. Florian, J.; Sponer, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 884-892.
102. Noy, A.; Perez, A.; Laughton, C. A.; Orozco, M. Nucleic Acids Res. 2007, 35, 3330-3338.
103. Vertessy, B. G.; Toth, J. Acc. Chem. Res. 2009, 42, 97-106.
104. Leontis, N. B.; Stombaugh, J.; Westhof, E. Nucleic Acids Res. 2002, 30, 3497-3531.
105. Sponer, J. E.; Leszczynski, J.; Sychrovsky, V.; Sponer, J. J. Phys. Chem. B 2005, 109, 18680-18689.
106. Kroonbatenburg, L. M. J.; Vanduijneveldt, F. B. J. Mol. Struct. (THEOCHEM) 1985, 22, 185-199.
107. Luo, R.; Gilson, H. S. R.; Potter, M. J.; Gilson, M. K. Biophys. J. 2001, 80, 140-148.
108. Mao, L. S.; Wang, Y. L.; Hu, X. C. J. Phys. Chem. B 2003, 107, 3963-3971.
109. Dracinsky, M.; Castano, O. Phys. Chem. Chem. Phys. 2004, 6, 1799-1805.
110. Cysewski, P.; Czyznikowska-Balcerak, Z.; Szefler, B. Pol. J. Chem. 2003, 77, 1287-1300.
111. Rutledge, L. R.; Wheaton, C. A.; Wetmore, S. D. Phys. Chem. Chem. Phys. 2007, 9, 497-509.
112. Rutledge, L. R.; Campbell-Verduyn, L. S.; Hunter, K. C.; Wetmore, S. D. J. Phys. Chem. B 2006, 110, 19652-19663.
113. Seio, K.; Ukawa, H.; Shohda, K.; Sekine, M. J. Biomol. Struct. Dyn. 2005, 22, 735-746.
114. Rauwolf, C.; Mehlhorn, A.; Fabian, J. Collect. Czech. Chem. Commun. 1998, 63, 1223-1244.
115. Alagona, G.; Ghio, C.; Monti, S. J. Phys. Chem. A 1998, 102, 6152-6160.
116. Lee, N. K.; Park, S.; Kim, S. K. J. Chem. Phys. 2002, 116, 7910-7917.
117. Wang, Y. L.; Hu, X. C. J. Chem. Phys. 2002, 117, 1-4.
118. Biot, C.; Buisine, E.; Kwasigroch, J. M.; Wintjens, R.; Rooman, M. J. Biol. Chem. 2002, 277, 40816-40822.
119. Wintjens, R.; Biot, C.; Rooman, M.; Lievin, J. J. Phys. Chem. A 2003, 107, 6249-6258.
120. McConnell, T. L.; Wetmore, S. D. J. Phys. Chem. B 2007, 111, 2999-3009.
121. Jurecka, P.; Sponer, J.; Hobza, P. J. Phys. Chem. B 2004, 108, 5466-5471.
122. Mathews, D. H.; Turner, D. H. Curr. Opin. Struct. Biol. 2006, 16, 270-278.
123. Mathews, D. H.; Disney, M. D.; Childs, J. L.; Schroeder, S. J.; Zuker, M.; Turner, D. H. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7287-7292.
124. Alexandrov, B. S.; Gelev, V.; Monisova, Y.; Alexandrov, L. B.; Bishop, A. R.; Rasmussen, K. O.; Usheva, A. Nucleic Acids Res., in press.
125. Warmlander, S.; Sponer, J. E.; Sponer, J.; Leijon, M. J. Biol. Chem. 2002, 277, 28491-28497.
126. Lankas, F.; Cheatham, T. E.; Spackova, N.; Hobza, P.; Langowski, J.; Sponer, J. Biophys. J. 2002, 82, 2592-2609.
127. Kopitz, H.; Zivkovic, A.; Engels, J. W.; Gohlke, H. Chem. Bio. Chem. 2008, 9, 2619-2622.