Structure-function studies on a synthetic guanosine receptor that simultaneously binds Watson-Crick and Hoogsteen sites

Journal of Organic Chemistry

Volumn 70, Issue 19, 2005, Pages 7459-7467

  Quinn, Jordan R ^a   Zimmerman, Steven C ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SYNTHESIS (CHEMICAL);

GUANOSINE RECEPTOR; STRUCTURE-FUNCTION STUDIES; WATSON-CRICK AND HOOGSTEEN SITES;

NITROGEN COMPOUNDS;

AMINONAPHTHALENE; AMINOQUINOLINE DERIVATIVE; CARBENE; CARBONYL DERIVATIVE; CHLOROFORM; CYTOSINE; DIMETHYL SULFOXIDE; DNA BASE; GUANOSINE; GUANOSINE DERIVATIVE; GUANOSINE RECEPTOR; GUANOSINE TRI O PENTANOATE; NAPHTHALENE DERIVATIVE; NITROGEN; NUCLEOSIDE ANALOG; RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; COMPLEX FORMATION; ENERGY TRANSFER; PROTEIN DNA BINDING; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ACTIVITY RELATION; SYNTHESIS;

DNA; DRUG DESIGN; GUANOSINE; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 24944509595     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo0501689     Document Type: Article

References (84)

1. (a) Seeman, N. C. Nature 2003, 421, 427-431.
2. (b) Storhoff, J. J.; Mirkin, C. A. Chem. Rev. 1999, 99, 1849-1862.
3. (c) Niemeyer, C. M. Angew. Chem., Int. Ed. Engl. 1997, 36, 585-587.
4. (a) Scherer, L. J.; Rossi, J. J. Nature Biotechnol. 2003, 21, 1457-1465.
5. (b) Therapeutic Oligonucleotides: Antisense, RNAi, Triple-Helix, Enhancer-Decoy, CpG, and DNA Chips; Cho-Chung, Y. S., Gewirtz, A. M., Stein, C. A., Eds. Ann. N.Y. Acad. Sci. 2003, 1002, 274 pp.
6. Verma, S.; Eckstein, F. Annu. Rev. Biochem. 1998, 67, 99-134.
7. Kool, E. T. Chem. Rev. 1997, 97, 1473-1487.
8. Herdewijn, P. Antisense Nucleic A. 2000, 10, 297-310.
9. Luyten, I.; Herdewijn, P. Eur. J. Med. Chem. 1998, 33, 515-576.
10. Selected reviews: Fan, E.; Hamilton, A. D. In Crystal Engineering: The Design and Application of Functional Solids; Seddon, K. R., Zaworotko, M., Eds.; Kluwer: Dordrecht, 1999; pp 357-369.
11. Hamilton, A. D.; Fan, E.; Van Arman, S.; Vicent, C.; Tellado, F. G.; Geib, S. J. Supramol. Chem. 1993, 1, 247-252.
12. Rebek, J., Jr. Top. Curr. Chem. 1988, 149, 189-210.
13. Wintner, E. A.; Conn, M. M.; Rebek, J., Jr. Acc. Chem. Res. 1994, 27, 198-203.
14. Hartley, J. H.; James, T. D.; Ward, C. J. J. Chem. Soc., Perkin Trans. 1 2000, 19, 3155-3184.
15. Beer, P. D.; Schmitt, P. Curr. Opin. Chem. Biol. 1997, 1, 475-482.
16. Sessler, J. L.; Sansom, P. I.; Andrievsky, A.; Kral, V. In Supramolecular Chemistry of Anions; Bianchi, A., Bowman-James, K., Garcia-Espana, E., Eds.; Wiley-VCH: New York, 1997; pp 355-419.
17. Davis, A. P. In Supramolecular Science: Where It Is and Where It Is Going; Ungaro, R., Dalcanale, E., Eds.; Kluwer: Dordrecht, 1999; pp 125-146.
18. Zimmerman, S. C.; Corbin, P. S. Struct. Bonding 2000, 96, 63-94.
19. Selected examples: Adrian, J. C.; Wilcox, C. S. J. Am. Chem. Soc. 1989, 111, 8055-8057.
20. Seel, C.; Vögtle, F. Angew. Chem., Int. Ed. Engl. 1991, 30, 442-444.
21. Deslongchamps, G.; Galán, A.; de Mendoza, J.; Rebek, J., Jr. Angew. Chem., Int. Ed. Engl. 1992, 31, 61-63.
22. Güther, R.; Nieger, M.; Vögtle, F. Angew. Chem., Int. Ed. Engl. 1993, 32, 601-603.
23. Kato, Y.; Conn, M. M.; Rebek, J., Jr. J. Am. Chem. Soc. 1994, 116, 3279-3284.
24. Bell, T. W.; Hou, Z.; Zimmerman, S. C.; Thiessen, P. A. Angew. Chem., Int. Ed. Engl. 1995, 34, 2163-2165.
25. Lonergan, D. G.; Deslongchamps, G.; Tomàs, S. Tetrahedron Lett. 1998, 39, 7861-7864.
26. Alkorta, I.; Elguero, J.; Goswami, S.; Mukherjee, R. J. Chem. Soc., Perkin Trans. 2 2002, 894-898.
27. Faraoni, R.; Blanzat, M.; Kubicek, S.; Braun, C.; Schweizer, W. B.; Gramlich, V.; Diederich, F. Org. Biomol. Chem. 2004, 2, 1962-1964.
28. A notable exception is the G-clamp, which forms two hydrogen bonds to the Hoogsteen side of G in addition to the standard three Watson-Crick hydrogen bonds: Lin, K.-Y.; Matteucci, M. D. J. Am. Chem. Soc. 1998, 120, 8531-8532.
29. Flanagan, W. M.; Wolf, J. J.; Olson, P.; Grant, D.; Lin, K.-Y.; Wagner, R. W.; Matteucci, M. D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 3513-3518.
30. Wilds, C. J.; Maier, M. A.; Tereshko, V.; Manoharan, M.; Egli, M. Angew. Chem., Int. Ed. 2002, 41, 115-117.
31. Wilds, C. J.; Maier, M. A.; Manoharan, M.; Egli, M. Helv. Chim. Acta 2003, 86, 966-978.
32. Amemiya, S.; Bühlmann, P.; Umezawa, Y. Chem. Commun. 1997, 1027-1028.
33. Tohda, K.; Amemiya, S.; Ohki, T.; Nagahora, S.; Tanaka, S.; Bühlmann, P.; Umezawa, Y. Isr. J. Chem. 1997, 37, 267-275.
34. (a) Busson, R.; Kerremans, L.; Van Aerschot, A.; Peeters, M.; Blaton, N.; Herdewijn, P. Nucleosides Nucleotides 1999, 18, 1079-1082.
35. (b) Wada, T.; Kobori, A.; Kawahara, S.; Sekine, M. Tetrahedron Lett. 1998, 39, 6907-6910.
36. Bz) prefers the intramolecularly hydrogen bonded syn-imino form (Wallis, M. P.; Schwalbe, C. H.; Fraser, W. Nucleosides Nucleotides 1997, 16, 2053-2068);
37. Bz derivatives: Schöning, K.-U.; Scholz, P.; Wu, X.; Guntha, S.; Delgado, G.; Krishnamurthy, R.; Eschenmoser, A. Helv. Chim. Acta 2002, 85, 4111-4153.
38. Rennenberg, D.; Leumann, C. J. J. Am. Chem. Soc. 2002, 124, 5993-6002.
39. Woźniak, L. A.; Wieczorek, M.; Pyzowski, J.; Majzner, W.; Stec, W. J. J. Org. Chem. 1998, 63, 5395-5402.
40. Shoup, R. R.; Miles, H. T.; Becker, E. D. J. Phys. Chem. 1972, 76, 64-70.
41. Engel, J. D.; von Hippel, P. H. Biochemistry 1974, 13, 4143-4158.
42. Wada, T.; Kobori, A.; Kawahara, S.; Sekine, M. Eur. J. Org. Chem. 2001, 4583-4593.
43. Parthasarathy, R.; Ginell, S. L.; De, N. C.; Chheda, G. B. Biochem. Biophys. Res. Commun. 1978, 83, 657-663.
44. Chang, S.-K.; Hamilton, A. D. J. Am. Chem. Soc. 1988, 110, 1318-1319.
45. Chang, S.-K.; Van Engen, D.; Fan, E.; Hamilton, A. D. J. Am. Chem. Soc. 1991, 113, 7640-7645.
46. Valenta, J. N.; Dixon, R. P.; Hamilton, A. D.; Weber, S. G. Anal. Chem. 1994, 66, 2397-2403.
47. (a) Carver, F. J.; Hunter, C. A.; Shannon, R. J. J. Chem. Soc., Chem. Commun. 1994, 1277-1280.
48. (b) Brooksby, P. A.; Hunter, C. A.; McQuillan, A. J.; Purvis, D. H.; Rowan, A. E.; Shannon, R. J.; Walsh, R. Angew. Chem., Int. Ed. Engl. 1994, 33, 2489-2491.
49. (c) Hunter, C. A.; Pervis, D. H. Angew. Chem., Int. Ed. Engl. 1992, 31, 792-795.
50. Chang, S.-Y.; Kim, H. S.; Chang, K.-J.; Jeong, K.-S. Org. Lett. 2004, 6, 181-184.
51. Goswami, S.; Mukherjee, R. Tetrahedron Lett. 1997, 38, 1619-1622.
52. For example: Lukin, O.; Recker, J.; Böhmer, A.; Müller, W. M.; Kubota, T.; Okamoto, Y.; Nieger, M.; Fröhlich, R.; Vögtle, F. Angew. Chem., Int. Ed. 2003, 42, 442-445.
53. Kidd, T. J.; Leigh, D. A.; Wilson, A. J. J. Am. Chem. Soc. 1999, 121, 1599-1600.
54. Raposo, C.; Crego, M.; Mussons, M. L.; Caballero, M. C.; Morán, J. R. Tetrahedron Lett. 1994, 35, 3409-3410.
55. Crego, M.; Raposo, C.; Caballero, M. C.; García, E.; Saez, J. G.; Morán, J. R. Tetrahedron Lett. 1992, 33, 7437-7440.
56. Crego, M.; Partearroyo, A.; Raposo, C.; Mussons, M. L.; López, J. L.; Alcázar, V.; Morán, J. R. Tetrahedron Lett. 1994, 35, 1435-1438.
57. Martin, M.; Raposo, C.; Almaraz, M.; Crego, M.; Caballero, C.; Grande, M.; Morán, J. R. Angew. Chem., Int. Ed. Engl. 1996, 35, 2386-2388.
58. Petersen, P. M.; Wu, W.; Fenlon, E. E.; Kim, S.; Zimmerman, S. C. Bioorg. Med. Chem. 1996, 4, 1107-1112.
59. van Straaten-Nijenhuis, W. F.; de Jong, F.; Reinhoudt, D. N.; Thummel, R. P.; Bell, T. W.; Liu, J. J. Membrane Sci. 1993, 82, 277-283.
60. Hegde, V.; Hung, C.-Y.; Madhukar, P.; Cunningham, R.; Höpfner, T.; Thummel, R. P. J. Am. Chem. Soc. 1993, 115, 872-878.
61. Hegde, V.; Madhukar, P.; Madura, J. D.; Thummel, R. P. J. Am. Chem. Soc. 1990, 112, 4549-4550.
62. Geib, S. J.; Hirst, S. C.; Vincent, C.; Hamilton, A. D. J. Chem. Soc., Chem. Soc. 1991, 1283-1285.
63. Hamuro, Y.; Geib, S. J.; Hamilton, A. D. J. Am. Chem. Soc. 1997, 119, 10587-10593.
64. López de la Paz, M.; Ellis, G.; Penadés, S.; Vicent, C. Tetrahedron Lett. 1997, 38, 1659-1662.
65. Crisp, G. T.; Jiang, Y.-L. Tetrahedron 1999, 55, 549-560.
66. Hammick, D. L. J. Chem. Soc. 1926, 1302-1304.
67. Roth, R.; Erlenmeyer, H. Helv. Chim. Acta 1954, 37, 1064-1068.
68. Yokoyama, A.; Ohwada, T.; Saito, S.; Shudo, K. Chem. Pharm. Bull. 1997, 45, 279-283.
69. For related derivatives, see: Sung, W. L. J. Org. Chem. 1982, 47, 3623-3628.
70. Zimmerman, S. C.; Schmitt, P. J. Am. Chem. Soc. 1995, 117, 10769-10770.
71. Mertz, E.; Mattei, S.; Zimmerman, S. C. Org. Lett. 2000, 2, 2931-2934.
72. Mertz, E.; Mattei, S.; Zimmerman, S. C. Bioorg. Med. Chem. 2004, 12, 1517-1526.
73. Williams, L. D.; Chawla, B.; Shaw, B. R. Biopolymers 1987, 26, 591-603.
74. Williams, N. G.; Williams, L. D.; Shaw, B. R. J. Am. Chem. Soc. 1989, 111, 7205-7209.
75. The self-association constant for guanosine could not be determined in this solvent system because nonlinear regression analysis did not converge on a solution.
76. Rosenberg, J. M.; Seeman, N. C.; Day, R. O.; Rich, A. J. Mol. Biol. 1976, 104, 145-167.
77. Connors, K. A. Binding Constants: The Measurement of Molecular Complex Stability; Wiley: New York, 1987.
78. Igolen, J.; Morin, C. J. Org. Chem. 1980, 45, 4802-4804.
79. Yousif, M. M.; Saeki, S.; Hamana, M. J. Heterocycl. Chem. 1980, 17, 1029.
80. Langry, K. C. Org. Prep. Proc. Int. 1994, 26, 429-438.
81. Yokoyama, A.; Ohwada, T.; Saito, S.; Shudo, K. Chem. Pharm. Bull. 1997, 45, 279-283.
82. Procedure adapted from: Trafelet, H.; Stulz, E.; Leumann, C. Helv. Chim. Acta 2001, 84, 87-105.
83. Ogilvie, K. K.; Beaucage, S. L.; Schifman, A. L.; Theriault, N. Y.; Sadana, K. L. Can. J. Chem. 1978, 56, 2768-2780.
84. Procedure adapted from: Sergueeva, Z. A.; Sergueev, D. S.; Shaw, B. R. Nucleosides and Nucleotides 2000, 19, 275-282.