Molecular dynamics study of oligonucleotides containing difluorotoluene

Journal of the American Chemical Society

Volumn 122, Issue 29, 2000, Pages 6891-6899

  Cubero, Elena ^a   Laughton, Charles A ^b   Javier Luque, F ^a   Orozco, Modesto ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FLUORIDE; OLIGONUCLEOTIDE; TOLUENE DERIVATIVE;

ARTICLE; DNA DETERMINATION; DNA REPLICATION; MOLECULAR DYNAMICS; MOLECULAR STABILITY; THERMODYNAMICS;

EID: 0034718074     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja000117n     Document Type: Article

References (35)

1. Kornberg, A.; Baker, T. A. DNA Replication, 2nd ed.; W. H. Freeman: New York.
2. Goodman, M. F.; Creighton, S.; Bloom, L. B.; Petruska, J. CriJ. Rev. Biochem. Mol. Biol. 1993, 28, 83.
3. Petruska, J.; Goodman, M. F.; Boosalis, M. S.; Sowers, L. C.; Cheons, C. Proc. Nat!. Acad. Sei. U.S.A. 1988, 85, 6252.
4. Echols, H.; Goodman, M. F. Anna. Rev. Biochem. 1991, 60, 477.
5. Johnson, K. A. Anint. Rev. Biochem. 1993, 62, 685.
6. Guckian, K. M.; Kool, E. T. Angew. Chem., Int. Ed. 1997, 36, 2825.
7. Moran, S.; Ren, R. X.-E; Kool, E. T. Proc. Natl. Acad. Sei. U.S.A. 1997, 94, 10506.
8. Liu, D.Y.; Moran, S.; Kool, E. T. Chem. Biol. 1997, 4. 919.
9. Moran, S.; Ren, R. X.-F.; Rumney, S.; Kool, E. T. J. Am. Chem. Soc. 1997, 779, 2056.
10. Evans, T. A.; Seddon, K. R. J. Chem. Soc., Chem. Commun. 1997, 2023.
11. Wang, X.; Houk, K. N. J. Chem. Soc., Chem. Commun. 1998, 2631.
12. Guckian, K. M.; Krugh, T. R.; Kool, E. T. Nature Struct. Biol. 1998, 5, 954.
13. Cubero, E.; Sherer, E. C; Luque, F. J.; Orozco, M.; Laughton, C. A. J. Am. Chem. Soc. 1999, 121, 8653.
14. Soliva, R.; Luque, F. J.; Orozco, M. Nucleic Acid. Res. 1999, 27, 2248.
15. Hemândez, B.; Soliva, R.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2000. Submitted for publication.
16. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E; Ross, W.S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 5, University of California: San Francisco, 1997.
17. Cheetham. T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193.
18. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
19. Amott, S.; Hukins, W. L.-Biochem. Biophys. Res. Commun. 1972, 47, 15(M.
20. Shields, G. C.; Laughton, C. A.; Orozco, M. J. Am. Chem. Soc. 1997, 119, 7463.
21. Jorgensen, W. L.; Chandresekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
22. Lavery, R.; Sklenar, J. J. Biomol. Struct. Dyn. 1988, 6, 63.
23. Shields, G.; Laughton, C. A.; Orozco, M. J. Am. Cheni. Soc. 1998, 120, 5895.
24. Ragunnathan, G.; Miles, H. T.; Sasisekharan, V. Biochemistry 1993, 32, 455.
25. Howard, F. N.; Miles, H, T.; Liu, K.; Frazier, J.; Raghunathan, G.; Sasisekharan, V. Biochemistry 1993, 31, 10671.
26. In all cases the gas phase profile is subtracted to produce a common reference state for all the simulations.
27. (a) Luque, F. J.; Nègre, M.; Orozco, M. J. Phys. Chem. 1993, 97, 4386.
28. (b) Luque, F. J.; Bachs, M.; Orozco, M. J. Compiit. Chem. 1994, 15, 847.
29. Orozco, M.; Bachs, M.; Luque, F. J. J. Comput. Chem. 1995, 16, 564-575.
30. Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.
31. (e) Miertus, J.; Tomasi, J. Chem. Phys. 1982, 05, 239.
32. AM1A1ST calculations show that hydration disfavors A-T and AF pairings by around 8.1 and 3.6 kcal/mol. This implies that solvation favors relative binding of F to A, with respect to the binding of T to A, by around 4.5 kcal/mol, thus reducing the apparent large difference in stability suggested from H-bonding considerations alone.
33. Marky, L. A.; Breslauer, K. J. Biopolymers 1987, 26, 1601.
34. B3LYP/6-31G(d, p) geometry optimization suggests stabilization energies (after BSSE correction) of -3.1, and -2.9 kcal/mol for Hoogsteen and Watson-Crick A-F pairs. These values are remarkably similar to those obtained using AMBER parameters: -3.3 (A-F, H) and -3.2 (A-F, WC) kcal/mol.
35. Roberts, R. W.; Crothers, D. M. Proc. Nail. Acad. Sei. U.S.A. 1996, 93, 4320.