Striving to understand the properties of universal nucleobases: A computational study of azole carboxamides

Journal of Physical Chemistry A

Volumn 107, Issue 39, 2003, Pages 7900-7910

  LaPointe, Shenna M ^a   Wetmore, Stacey D ^a  

^a MOUNT ALLISON UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AZOLE CARBOXAMIDES; NUCLEOBASES;

BINDING ENERGY; HYDROGEN BONDS; MOLECULES; NUMERICAL METHODS; ORGANIC COMPOUNDS; PROBABILITY DENSITY FUNCTION; RNA;

DNA;

EID: 0142040148     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp035000a     Document Type: Article

References (107)

1. Saiki, R.; Scharf, S.; Faloona, F.; Mullis, K.; Horn, C.; Erlich, H.; Arnheim, N. Science 1985, 230, 1350-1354.
2. For a review of antigene (antisense) therapeutic strategies, see, for example, (a) Uhlmann, E.; Peyman, A. Chem. Rev. 1990, 90, 543-584.
3. (b) Antisense Strategies; Baserga, R., Denhardt, D. T., Eds.; Ann. N.Y. Acad. Sci. 1992, 660, 1.
4. (c) Milligan, J. F.; Matteucci, M. D.; Martin, J. C. J. Med. Chem. 36, 1923-1937.
5. (d) De Mesmaeker, A.; Häner, R.; Martin, P.; Moser, H. E. Acc. Chem. Res. 1995, 28, 366-374.
6. (e) Kvaernø, L.; Wengel J. Chem. Commun. 2001, 1419-1424.
7. For a review of the literature of universal bases (to 2000) including modifications considered and their applications, see Loakes, D. Nucleic Acids Res. 2001, 29, 2437-2447.
8. Ohtsuka. E.; Matsuki, S.; Ikehara, M.; Takahashi, Y.; Matsubara, K. J. Biol. Chem. 1985, 260, 2605-2608.
9. (a) Martin, F. H.; Castro, M. M.; Aboul-ela, F.; Tinoco, I. Nucleic Acids Res. 1985, 13, 8927-8938.
10. Takahashi, Y.; Kato, K.; Hayashizaki, Y.; Wakabayashi, T.; Ohtsuka, E.; Matsuki, S.; Ikehara, M.; Kenichi, M. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 1931-1935.
11. (c) Kawase, Y.; Iwai, S.; Inoue, H.; Miura, K.; Ohtsuka, E. Nucleic Acids Res. 1986, 14, 7727-7736.
12. (d) Corfield, P. W. R.; Hunter, W. N.; Brown, T.; Robinson, P.; Kennard, O. Nucleic Acids Res. 1987, 15, 7935-7949.
13. (e) Uesugi, S.; Oda, Y.; Ikehara, M.; Kawase, Y.; Ohtsuka, E. J. Biol. Chem. 1987, 262, 6965-6968.
14. (f) Patil, R. V.; Dekker, E. E. Nucleic Acids Res. 1990, 18, 3080.
15. (g) Batzer, M. A.; Carlton, J. E.; Deininger, P. L. Nucleic Acids Res. 1991, 19, 5081.
16. (h) Kamiya, H.; Sakaguchi, T.; Murata, N.;Fujimuro, M.; Miura, H.; Ishikawa, K.; Shimizu, M.; Inoue, H.; Nishimura, S.; Matsukage, A.; Masutani, C.; Hanaoka, F.; Ohtsuka, E. Chem. Pharm. Bull. 1992, 40, 2792-2795.
17. (i) Case-Green, S. C.; Southern, E. M. Nucleic Acids Res. 1994, 22, 131.
18. Zhang, P.; Johnson, W. T.; Klewer, D.; Paul, N.; Hoops, G.; Davisson, V. J.; Bergstrom, D. E. Nucleic Acids Res. 1998, 26, 2208-2215.
19. (a) Millican, T. A.; Mock, G. A.; Chauncey, M. A.; Patel, T. P.; Eaton, M. A. W.; Gunning, J.; Cutbush, S. D.; Neidle, S.; Mann, J. Nucleic Acids Res. 1984, 12, 7435-7453.
20. (b) Francoise, P.; Perilleux, D.; Kempener, Y.; Sonveaux, E. Tetrahedron Lett. 1990, 31, 6347-6350.
21. Bergstrom, D. E.; Zhang, P.; Johnson, W. T. Nucleic Acids Res. 1997, 25, 1935-1942.
22. (a) Nichols, R.; Andrews, P. C.; Zhang, P.; Bergstrom, D. E. Nature 1994, 369, 492-493.
23. (b) Bergstrom, D. E.; Zhang, P.; Toma, P. H.; Andrews, P. C.; Nichols, R. J. Am. Chem. Soc. 1995, 117, 1201-1209.
24. (c) Amosova, O.; George, J.; Fresco, J. R. Nucleic Acids Res. 1997, 25, 1930-1934.
25. (d) Klewer, D. A.; Hoskins, A.; Zhang, P.; Davisson, V. J.; Bergstrom, D. E.; LiWang, A. C. Nucleic Acids Res. 2000, 28, 4514-4522.
26. (e) Oliver, J. S.; Parker, K. A.; Suggs, J. W. Org. Lett. 2001, 3, 1977-1980.
27. (a) Loakes, D.; Brown, D. M. Nucleic Acids Res. 1994, 20, 4039-4043.
28. (b) Loakes, D.; Hill, F.; Linde, S.; Brown, D. M. Nucleosides Nucleotides 1995, 14, 1001-1003.
29. (c) Loakes, D.; Brown, D. M.; Linde, S.; Hill, F. Nucleic Acids Res. 1995, 23, 2361-2366.
30. (d) Loakes, D.; Hill, F.; Brown, D. M.; Salisbury, S. A. J. Mol. Biol. 1997, 270, 426-435.
31. (a) Van Aerschot, A.; Rozenski, J.; Loakes, D.; Pillet, N.; Schepers, G.; Herdewijn, P. Nucleic Acids Res. 1995, 23, 4363-4370.
32. (b) Van Aerschot, A.; Hendrix, C.; Schepers, G.; Pillet, N.; Herdewijin, P. Nucleosides Nucleotides 1995, 14, 1053-1056.
33. Seela, F.; Bourgeois, W.; Rosemeyer, H.; Wenzel, T. Helv. Chim. Acta 1996, 79, 488-498.
34. (a) Matray, T. J.; Kool, E. T. J. Am. Chem. Soc. 1998, 120, 6191-6192.
35. (b) Morales, J. C.; Kool, E. T. Nat. Struct. Biol. 1998, 5, 950-954.
36. (c) McMinn, D. L.; Ogawa, A. K.; Wu, Y.; Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 1999, 121, 11585-11586.
37. (d) Ogawa, A. K.; Wu, Y.; McMinn, D. L.; Liu, J.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 3274-3287.
38. (e) Ogawa, A. K.; Wu, Y.; Berger, M.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 8803-8804.
39. (f) Wu, Y.; Ogawa, A. K.; Berger, M.; McMinn, D. L.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2000, 122, 7621-7632.
40. (g) Berger, M.; Ogawa, A. K.; McMinn, D. L.; Wu, Y.; Schultz, P. G.; Romesberg, F. E. Angew. Chem. Int. Ed. 2000, 39, 2940-2942.
41. (h) Berger, M.; Wu, Y.; Ogawa, A. K.; McMinn, D. L.; Schultz, P. G.; Romesberg, F. E. Nucleic Acids Res. 2000, 28, 2911-2914.
42. (i) Lee, E.; Wu, Y.; Xia, G.; Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2001, 123, 7439-1440.
43. (j) Berger, M.; Luzzi, S. D.; Henry, A. A.; Romesberg, F. E. J. Am. Chem. Soc. 2002, 124, 1222-1226.
44. (k) Wu, Y.; Fa, M.; Tae, E. L.: Schultz, P. G.; Romesberg, F. E. J. Am. Chem. Soc. 2002, 124, 14626-14630.
45. (l) O'Neill, B. M.; Ratto, J. E.; Good, K. L.; Tahmassebi, D. C.; Helquist, S. A.; Morales, J. C.; Kool, E. T. J. Org. Chem. 2002, 67, 5869-5875.
46. (a) Challa, H.; Styers, M. L.: Woski, S. A. Org. Lett. 1999, 1, 1639-1641.
47. (b) Babu, B. R.; Wengel, J. Chem. Commun. 2001, 20, 2114-2115.
48. Bergstrom, D. E.; Zhang, P.; Zhou, J. J. Chem. Soc., Perkin. Trans 1 1994, 3029-3034.
49. Bergstrom, D. E.; Zhang, P.; Johnson, W. T. Nucleosides Nucleotides 1996, 15, 59-68.
50. Pochet, S.; Dugue, L.; Meier, A.; Marliere, P. Bioorg. Med. Chem. Lett. 1995, 5, 1679-1684.
51. Sala, M.; Pezo, V.; Pochet, S.; Wain-Hobson, S. Nucleic Acids Res. 1996, 24, 3302-3306.
52. Johnson, W. T.; Zhang, P.; Bergstrom, D. E. Nucleic Acids Res. 1997, 25, 559-567.
53. Hoops, G. C.; Zhang, P.; Johnson, W. T.; Paul, N.; Bergstrom, D. E.; Davisson, V. J. Nucleic Acids Res. 1997, 25, 4866-4871.
54. Pochet, S.; Dugue, L. Nucleosides Nucleotides 1998, 17, 2003-2009.
55. Loakes, D.; Guo, M. J.; Brown, D. M.; Salisbury, S. A.; Smith, C. L.; Felix, I.; Kumar, S.; Nampalli, S. Nucleosides, Nucleotides Nucleic Acids 2000, 19, 1599-1614.
56. Klewer, D. A.; Zhang, P.; Bergstrom, D. E.; Davisson, V. J.; LiWang, A. C. Biochemistry 2001, 40, 1518-1527.
57. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 553.
58. For a review of theoretical calculations on hydrogen-bonded systems, see Scheiner, S. Hydrogen Bonding: A Theoretical Perspective; Oxford University Press: New York, 1997.
59. (a) van Lenthe, J. H.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Duijneveldt, F. B. Adv. Chem. Phys. 1987, 69, 521.
60. (b) Chalasinski, G.; Gutowski, M. Chem. Rev. 1988, 943.
61. (c) Scheiner, S. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers: New York, 1991; Vol. 2, p 165.
62. (d) Mourik, T. V.; Wilson, A. K.; Peterson, K. A.; Woon, D. E.; Dunning, T. H., Jr. Adv. Quantum Chem. 1998, 31, 105.
63. (e) Kestner, N. R.; Combariza, J. E. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B.; Eds.; VCH Publishers: New York, 1999; Vol. 13, p 99.
64. (a) Hobza, P., Sponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315.
65. (b) Del Bene, J. E.; Person, W. B.; Szczepaniak, K. J. Phys. Chem. 1995, 99, 10705.
66. (c) Civalleri, B.; Garrone, E.; Ugliengo, P. J. Mol. Struct.: THEOCHEM 1997, 419, 227.
67. (d) Maerker, C.; von Ragué Schleyer, P.; Leidl, K. R.; Ha, T.-K.; Quack, M.; Suhm, M. A. J. Comput. Chem. 1997, 18, 1695.
68. (e) Paiz, B.; Suhai, S. J. Comput. Chem. 1998, 19, 575.
69. (f) Rappé, A. K.; Bernstein, E. R. J. Phys. Chem. A 2000, 104, 6117.
70. (a) Sim, F.; St-Amant, A.; Pápai, I.; Salahub, D. R. J. Am. Chem. Soc. 1992, 114, 4391.
71. (b) Keininger, M.; Suhai, S. Int. J. Quantum Chem. 1994, 52, 465.
72. (c) Kim, K.; Jordan, K. D. J. Phys. Chem. 1994, 98, 10089.
73. (d) Latajka, Z.; Bouteiller, Y. J. Chem. Phys. 1994, 101, 9793.
74. (e) Mele, F.; Mineva, T.; Russo, N. Toscano, M. Theor. Chim. Acta 1995, 91, 169.
75. (f) Han, W.-G.; Suhai, J. Phys. Chem. 1996, 100, 3942.
76. (g) Lundell, J.; Latajka, Z. J. Phys. Chem. A 1997, 101, 5004.
77. (h) Lozynski, M.; Rusinska-Roszak, D.; Mack, H.-G. J. Phys. Chem. A 1998, 102, 2899.
78. (i) Chandra, A. K.; Nguyen, M. T. Chem. Phys. 1998, 232, 299.
79. (j) McAllister, M. A. J. Mol. Struct.: THEOCHEM 1998, 427, 39.
80. (k) Rablen, P. R.; Lockman, J. W.; Jorgensen, W. L. J. Phys. Chem. A 1998, 102, 3782.
81. (l) Pan, Y.; McAllister, M. A. J. Mol. Struct.: THEOCHEM 1998, 427, p 221.
82. (m) Hartmann, M.; Wetmore, S. D.; Radom, L. J. Phys. Chem. 2001, 105, 4470-4479.
83. (n) Wetmore, S. D.; Schofield, R.; Smith, D. M.; Radom, L. J. Phys. Chem. 2001, 105, 8718-8726.
84. Sponer, J.; Leszczynski, J. J. Phys. Chem. 1996, 100, 1965-1974.
85. (a) Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2001, 105, 10115-10123.
86. (b) Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. A 2002, 106, 9345-9351.
87. (c) Reynisson, J.; Steenken, S. Phys. Chem. Chem. Phys. 2002, 4, 5353-5358.
88. (d) Reynisson, J.; Steenken, S. Phys. Chem. Chem. Phys. 2002, 4, 5346-5353.
89. (e) Richardson, N. A.; Wesolowski, S. S.; Schaefer, H. F. J. Phys. Chem. B 2003, 107, 848-853.
90. Kawahara, S.; Wada, T.; Kawauchi, S.; Uchimaru, T.; Sekine, M. J. Phys. Chem. A 103, 8516-8523.
91. Podolyan, Y.; Rubin, Y. V.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 9964-9970.
92. (a) Nguyen, M. T.; Chandra, A. K.; Zeegers-Huyskens, T. J. Chem. Soc., Faraday Trans. 1998, 94, 1277-1280.
93. (b) Chandra, A. K.; Nguyen, M. T.; Uchimaru, T.; Zeegers-Huyskens, T. J. Phys. Chem. A 1999, 103, 8853-8860.
94. (c) Kryachko, E. S.; Nguyen, M. T.; Zeegers-Huyskens, T. J. Phys. Chem. A 2001, 105, 1934-1943.
95. (d) Gaigeot, M. P.; Ghomi, M. J. Phys. Chem. B 2001, 105, 5007-5017.
96. (e) Sukhanov, O. S.; Shishkin, O. V.; Gorb, L.; Podolyan, Y.; Leszczynski, J. J. Phys. Chem. B 2003, 107, 2846-2852.
97. (a) Foloppe, N.; MacKerell, A. D. J. Phys. Chem. B 1998, 102, 6669-6678
98. (b) Brameld, K. A.; Goddard, W. A. J. Am. Chem. Soc. 1999, 121, 985-993
99. (c) Foloppe, N.; Nilsson, L.; MacKerell, A. D. Biopolymers (Nucleic Acid Sci.) 2002, 61, 61-76 and references therein.
100. We note that the conformation of the X = Y = C, Z = N azole carboxamide that Johnson et al. refer to as anti corresponds to our syn-t conformer. For consistency, we use the same nomenclature for all azole carboxamides (Scheme 2).
101. SCF(rel), Table 2, ref 25) indicate that the syn conformer is more stable. Our calculations indicate that the syn-t conformer is more stable for this azole carboxamide (Table 1).
102. The glycosyl torsion angle (Χ) is defined as ∠(01'C1'N1C2) in pyrimidine and ∠(O1'C1'N9C4) in purine nucleotide. This dihedral angle ranges from 90 to 270° for the anti conformation typically found in A-DNA and B-DNA in right-handed and left-handed nucleic acid helices. χ varies between +90 and -90° for the syn orientation often found in left-handed (Z-form) helices of DNA and RNA. (See Saenger, W. Principles of Nucleic Acid Structure; Cantor, C. R., Ed.; Springer-Verlag: New York, 1984).
103. We note that Klewer et al. report that molecular modeling of the X = Z = N, Y = CH azole carboxamide contained within a DNA duplex reveals that this molecule cannot adequately pair with adenine or cytosine.
104. It should be noted that Klewer et al. report a conformational exchange about τ when the X = Z = N, Y = CH azole carboxamide is paired opposite guanine.
105. It should also be noted that calculations predict that this azole carboxamide forms a distorted pair with adenine; therefore, binding to adenine is expected to be unfavorable.
106. We note that cytosine interacts with the anti-τ conformer, which is slightly less stable that the syn-τ conformer that interacts with thymine. However, even if this energy difference is taken into account, the binding strength of the cytosine pair is still greater than that of the corresponding thymine pair.
107. It should be noted that Klewer et al. suggested that differences in stabilities observed experimentally for the X = Z = N, Y = CH azole carboxamide may actually be due to differences in intrastrand sequences introduced by changing the pairing sequence.