Molecular design, chemical synthesis, and evaluation of cytosine-carbohydrate hybrids for selective recognition of a single guanine bulged duplex DNA

Bioorganic and Medicinal Chemistry Letters

Volumn 15, Issue 19, 2005, Pages 4332-4335

  Idutsu, Yusuke ^a   Sasaki, Ayaka ^a   Matsumura, Shuichi ^a   Toshima, Kazunobu ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Bulge; Carbohydrate; DNA; Molecular recognition; Nucleotide base

Indexed keywords

CARBOHYDRATE; COMPLEMENTARY DNA; CYTOSINE; DNA BASE; DNA HYBRID; DOUBLE STRANDED DNA; GUANINE; NUCLEOTIDE;

ARTICLE; HYBRID; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; SYNTHESIS;

BASE PAIR MISMATCH; BINDING SITES; CARBOHYDRATES; CYTOSINE; DNA; DRUG DESIGN; GUANINE; INTERCALATING AGENTS; MOLECULAR PROBES; NUCLEIC ACID DENATURATION; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE;

EID: 23944473181     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2005.06.073     Document Type: Article

References (30)

1. D. Turner Curr. Opin. Struct. Biol. 2 1992 334
2. G. Streisinger, and J. Owen Genetics 109 1985 633
3. S.A. Woodson, and D.M. Crothers Biochemistry 26 1987 904
4. S.A. Woodson, and D.M. Crothers Biochemistry 27 1988 436
5. Y.-H. Wang, C.D. Bortner, and J. Griffith J. Biol. Chem. 268 1993 17571
6. V.A. Malkov, I. Biswas, R.D. Camerini-Otero, and P. Hsieh J. Biol. Chem. 272 1997 23811
7. J.W. Nelson, and I. Tinoco Jr. Biochemistry 24 1985 6416
8. S.A. White, and D.E. Draper Nucleic Acids Res. 15 1987 4049
9. S.A. Woodson, and D.M. Crothers Biochemistry 27 1988 8904
10. L.D. Williams, and I.H. Goldberg Biochemistry 27 1988 3004
11. C.J. Cortes, and H.-J. Wang Biochemistry 35 1996 616
12. K. Nakatani, A. Okamoto, and I. Saito Angew. Chem., Int. Ed. 38 1999 3378
13. Z. Xi, G.-S. Hwang, I.H. Goldberg, J.L. Harris, W.T. Pennington, F.S. Fouad, G. Qabaja, J.M. Wright, and G.B. Jones Chem. Biol. 9 2002 925
14. M.L. Colgrave, H.E.L. Williams, and M.S. Searle Angew. Chem., Int. Ed. 41 2002 4754
15. K. Nakatani, S. Sando, and I. Saito J. Am. Chem. Soc. 122 2000 2172
16. K. Nakatani, S. Horie, T. Murase, S. Hagihara, and I. Saito Bioorg. Med. Chem. 11 2003 2347
17. K. Nakatani, S. Horie, and I. Saito J. Am. Chem. Soc. 125 2003 8972
18. K. Toshima, H. Ouchi, Y. Okazaki, T. Kano, M. Moriguchi, A. Asai, and S. Matusumura Angew. Chem., Int. Ed. 36 1997 2748
19. K. Toshima, R. Takano, Y. Maeda, M. Suzuki, A. Asai, and S. Matsumura Angew. Chem., Int. Ed. 38 1999 3733
20. K. Toshima, Y. Maeda, H. Ouchi, A. Asai, and S. Matsumura Bioorg. Med. Chem. Lett. 10 2000 2163
21. K. Toshima, Y. Okuno, Y. Nakajima, and S. Matsumura Bioorg. Med. Chem. Lett. 12 2002 671
22. K. Toshima, R. Takano, T. Ozawa, and S. Matsumura Chem. Commun. 2002 212
23. K. Toshima, G. Matsuo, and K. Tatsuta Tetrahedron Lett. 33 1992 2175
24. H. Vorbruggen, K. Krolikiewicz, and B. Bennua Chem. Ber. 114 1981 1256
25. The synthesis of 2 will be reported in detail elsewhere.
26. 4; J Hz) data for 1 and 2. Compound 1: δ 1.33 (3H, d, J = 6.0), 1.62 (1H, ddd, J = 12.0, 12.0, and 10.0), 2.08 (1H, ddd, J = 12.0, 4.0, and 2.0), 2.37 (6H, s), 2.78 (1H, ddd, J = 12.0, 9.0, and 4.0), 3.21 (1H, dd, J = 9.8 and 9.8), 3.47 (1H, dq, J = 9.8 and 6.0), 5.72 (1H, dd, J = 10.0 and 2.0), 5.91 (1H, d, J = 8.0), 7.70 (1H, d, J = 8.0). Compound 2: δ 1.29 (3H, d, J = 6.0), 1.66 (1H, ddd, J = 12.0, 12.0, and 9.0), 2.23 (1H, ddd, J = 12.0, 4.0, and 2.0), 2.75-2.90 (1H, m), 2.79 (3H, s), 2.86 (3H, s), 3.20-3.40 (3H, m), 3.67 (1H, dq, J = 9.8 and 6.0), 3.82-3.95 (1H, m), 4.0-4.10 (1H, m), 4.65 (1H, dd, J = 9.0 and 2.0), 6.01 (1H, d, J = 8.0), 7.85 (1H, d, J = 8.0).
27. S. Walker, K.G. Valentine, and D. Kahne J. Am. Chem. Soc. 112 1990 6428
28. W. Ding, and G.A. Ellestad J. Am. Chem. Soc. 113 1991 6617
29. M. Uesugi, and Y. Sugiura Biochemistry 32 1993 4622
30. m value (0.7°) was very similar to those of 2 and 3 and lower than that of 1 under similar conditions.