Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: Molecular dynamics thermodynamics integration study

Journal of Physical Chemistry B

Volumn 117, Issue 6, 2013, Pages 1872-1879

  Krepl, Miroslav ^a   Otyepka, Michal ^b   Banáš, Pavel ^a,b   Šponer, Jiří ^a,c  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b PALACKÝ UNIVERSITY   (Czech Republic)

^c CENTRAL EUROPEAN INSTITUTE OF TECHNOLOGY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ELECTROSTATICS; EXPERIMENTS; FREE ENERGY; MOLECULAR DYNAMICS; POSITIVE IONS; RNA; THERMODYNAMICS;

AMINO GROUP; ATOMIC GROUPS; BALANCE OF ENERGIES; BASE PAIRS; CONTEXT DEPENDENT; DIFFERENT EFFECTS; ELECTROSTATIC POTENTIALS; ENERGY IMPACT; EXPLICIT SOLVENT MOLECULAR DYNAMICS; FREE ENERGY CHANGE; FREE ENERGY COMPUTATIONS; H-BONDS; INOSINE; INTRINSIC STRENGTH; NEGATIVELY CHARGED; QUALITATIVE DIFFERENCES; RNA DUPLEXES; SALT DEPENDENCE; THERMODYNAMICS EFFECTS; THERMODYNAMICS INTEGRATIONS;

IODINE;

EID: 84873892798     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp311180u     Document Type: Article

References (72)

1. Breaker, R. R. Nature 2004, 432, 838-845
2. RNA 3D Structure Analysis and Prediction; Leontis, N. B.; Westhof, E., Eds; Springer-Verlag: Berlin, Heidelberg, Germany, 2012.
3. Brion, P.; Westhof, E. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 113-137
4. Sponer, J.; Sponer, J. E.; Petrov, A. I.; Leontis, N. B. J. Phys. Chem. B 2010, 114, 15723-15741
5. Mathews, D. H.; Turner, D. H. Curr. Opin. Struct. Biol. 2006, 16, 270-278
6. Deigan, K. E.; Li, T. W.; Mathews, D. H.; Weeks, K. M. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 97-102
7. Mathews, D. H.; Sabina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288, 911-940
8. SantaLucia, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460-1465
9. Turner, D. H.; Sugimoto, N.; Kierzek, R.; Dreiker, S. D. J. Am. Chem. Soc. 1987, 109, 3783-3785
10. Kierzek, R.; Burkard, M. E.; Turner, D. H. Biochemistry 1999, 38, 14214-14223
11. Chen, J. L.; Dishler, A. L.; Kennedy, S. D.; Yildirim, I.; Liu, B.; Turner, D. H.; Serra, M. J. Biochemistry 2012, 51, 3508-3522
12. Yildirim, I.; Turner, D. H. Biochemistry 2005, 44, 13225-13234
13. Morgado, C. A.; Svozil, D.; Turner, D. H.; Sponer, J. Phys. Chem. Chem. Phys. 2012, 14, 12580-12591
14. Sponer, J.; Morgado, C. A.; Svozil, D. J. Phys. Chem. B 2012, 116, 8331-8332
15. Svozil, D.; Hobza, P.; Sponer, J. J. Phys. Chem. B 2010, 114, 1191-1203
16. Siegfried, N. A.; Kierzek, R.; Bevilacqua, P. C. J. Am. Chem. Soc. 2010, 132, 5342-5344
17. Spackova, N.; Berger, I.; Egli, M.; Sponer, J. J. Am. Chem. Soc. 1998, 120, 6147-6151
18. Gallego, J.; Golden, E. B.; Stanley, D. E.; Reid, B. R. J. Mol. Biol. 1999, 285, 1039-1052
19. Soliva, R.; Laughton, C. A.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1998, 120, 11226-11233
20. Spasic, A.; Serafini, J.; Mathews, D. H. J. Chem. Theory Comput. 2012, 8, 2497-2505
21. Koller, A. N.; Bozilovic, J.; Engels, J. W.; Gohlke, H. Nucleic Acids Res. 2010, 38, 3133-3146
22. Kopitz, H.; Zivkovic, A.; Engels, J. W.; Gohlke, H. Chembiochem 2008, 9, 2619-2622
23. Yildirim, I.; Stern, H. A.; Sponer, J.; Spackova, N.; Turner, D. H. J. Chem. Theory Comput. 2009, 5, 2088-2100
24. Beierlein, F. R.; Kneale, G. G.; Clark, T. Biophys. J. 2011, 101, 1130-1138
25. Cubero, E.; Laughton, C. A.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2000, 122, 6891-6899
26. Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B 2000, 104, 10092-10099
27. Hernandez, B.; Soliva, R.; Luque, F. J.; Orozco, M. Nucleic Acids Res. 2000, 28, 4873-4883
28. Spackova, N.; Cubero, E.; Sponer, J.; Orozco, M. J. Am. Chem. Soc. 2004, 126, 14642-14650
29. Di Cera, E. Chem. Rev. 1998, 98, 1563-1591
30. Klostermeier, D.; Millar, D. P. Biochemistry 2002, 41, 14095-14102
31. Siegfried, N. A.; Metzger, S. L.; Bevilacqua, P. C. Biochemistry 2007, 46, 172-181
32. Anderson, C. F.; Record, M. T. Annu. Rev. Phys. Chem. 1995, 46, 657-700
33. Sun, Z. H.; McLaughlin, L. W. Biopolymers 2007, 87, 183-195
34. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 1965-1974
35. Lankas, F.; Cheatham, T. E.; Spackova, N.; Hobza, P.; Langowski, J.; Sponer, J. Biophys. J. 2002, 82, 2592-2609
36. Bailly, C.; Mollegaard, N. E.; Nielsen, P. E.; Waring, M. J. EMBO J. 1995, 14, 2121-2131
37. Sherer, E. C.; Harris, S. A.; Soliva, R.; Orozco, H.; Laughton, C. A. J. Am. Chem. Soc. 1999, 121, 5981-5991
38. ShatzkySchwartz, M.; Arbuckle, N. D.; Eisenstein, M.; Rabinovich, D.; BareketSamish, A.; Haran, T. E.; Luisi, B. F.; Shakked, Z. J. Mol. Biol. 1997, 267, 595-623
39. Gros, J.; Rosu, F.; Amrane, S.; De Cian, A.; Gabelica, V.; Lacroix, L.; Mergny, J. L. Nucleic Acids Res. 2007, 35, 3064-3075
40. Strobel, S. A.; Shetty, K. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2903-2908
41. Rao, S. T.; Sundaralingam, M. J. Am. Chem. Soc. 1969, 91, 1210-1217
42. Kollman, P. Chem. Rev. 1993, 93, 2395-2417
43. Beutler, T. C.; Mark, A. E.; Vanschaik, R. C.; Gerber, P. R.; Vangunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529-539
44. Frisch, M. J. T., G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision A.2; Gaussian, Inc.: Wallingford CT, 2009.
45. Dennington, R. K., T.; Millam, J. GaussView, version 5; Semichem Inc.: Shawnee Mission, KS, 2009.
46. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; AMBER 12; University of California: San Francisco, CA, 2012.
47. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
48. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197
49. Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham, T. E.; Sponer, J.; Otyepka, M. J. Chem. Theory Comput. 2010, 6, 3836-3849
50. Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T. E.; Jurecka, P. J. Chem. Theory Comput. 2011, 7, 2886-2902
51. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
52. Aqvist, J. J. Phys. Chem. 1990, 94, 8021-8024
53. Smith, D. E.; Dang, L. X. J. Chem. Phys. 1994, 100, 3757-3766
54. Auffinger, P.; Cheatham, T. E.; Vaiana, A. C. J. Chem. Theory Comput. 2007, 3, 1851-1859
55. Joung, I. S.; Cheatham, T. E. J. Phys. Chem. B 2008, 112, 9020-9041
56. Adelman, S. A.; Doll, J. D. J. Chem. Phys. 1976, 64, 2375-2388
57. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
58. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
59. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
60. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
61. Steinbrecher, T.; Mobley, D. L.; Case, D. A. J. Chem. Phys. 2007, 127, 214108
62. Steinbrecher, T.; Joung, I.; Case, D. A. J. Comput. Chem. 2011, 32, 3253-3263
63. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1-41
64. Sponer, J.; Cang, X. H.; Cheatham, T. E. Methods 2012, 57, 25-39
65. Sponer, J.; Jurecka, P.; Hobza, P. J. Am. Chem. Soc. 2004, 126, 10142-10151
66. Takatani, T.; Hohenstein, E. G.; Malagoli, M.; Marshall, M. S.; Sherrill, C. D. J. Chem. Phys. 2010, 132, 144104
67. Sponer, J.; Kypr, J. Int. J. Biol. Macromol. 1994, 16, 3-6
68. Yildirim, I.; Stern, H. A.; Tubbs, J. D.; Kennedy, S. D.; Turner, D. H. J. Phys. Chem. B 2011, 115, 9261-9270
69. Besseova, I.; Banas, P.; Kuhrova, P.; Kosinova, P.; Otyepka, M.; Sponer, J. J. Phys. Chem. B 2012, 116, 9899-9916
70. Chen, A. A.; Draper, D. E.; Pappu, R. V. J. Mol. Biol. 2009, 390, 805-819
71. Krasovska, M. V.; Sefcikova, J.; Reblova, K.; Schneider, B.; Walter, N. G.; Sponer, J. Biophys. J. 2006, 91, 626-638
72. Bowman, J. C.; Lenz, T. K.; Hud, N. V.; Williams, L. D. Curr. Opin. Struct. Biol. 2012, 22, 262-272