Recognition of seven base pair sequences in the minor groove of DNA by ten-ring pyrrole-imidazole polyamide hairpins

Journal of the American Chemical Society

Volumn 119, Issue 33, 1997, Pages 7636-7644

  Turner, James M ^a   Baird, Eldon E ^a   Dervan, Peter B ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMIDAZOLE; POLYAMIDE; PYRROLE;

AFFINITY CHROMATOGRAPHY; ARTICLE; BINDING AFFINITY; BINDING SITE; DNA BINDING; DNA HELIX; DNA SEQUENCE; NUCLEOTIDE SEQUENCE;

EID: 0030953342     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja971208w     Document Type: Article

References (38)

1. Trauger, J. W.; Baird, E. E.; Dervan, P. B. Nature 1996, 382, 559.
2. (a) Wade, W. S.; Mrksich, M.; Dervan, P. B. J. Am. Chem. Soc. 1992, 114, 8783.
3. (b) Mrksich, M.; Wade, W. S.; Dwyer, T. J.; Geierstanger, B. H.; Wemmer, D. E.; Dervan, P. B. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 7586.
4. (c) Wade, W. S.; Mrksich, M.; Dervan, P. B. Biochemistry 1993, 32, 11385.
5. (a) Pelton, J. G.; Wemmer, D. E. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5723.
6. (b) Pelton, J. G.; Wemmer, D. E. J. Am. Chem. Soc. 1990, 112, 1393.
7. (c) Chen, X.; Ramakrishnan, B.; Rao, S. T.; Sundaralingham, M. Nature Struct. Biol. 1994, 1, 169.
8. (d) White, S.; Baird, E. E.; Dervan, P. B. Biochemistry 1996, 35, 12532.
9. Gottesfield, J. M.; Nealy, L.; Trauger, J. W.; Baird, E. E.; Dervan, P. B. Nature 1997, 387, 202.
10. Kelly, J. J.; Baird, E. E.; Dervan, P. B. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6981.
11. (a) Mrksich, M; Dervan, P. B. J. Am. Chem. Soc. 1993, 115, 2572.
12. (b) Geierstanger, B. H.; Dwyer, T. J.; Bathini, Y.; Lown, J. W.; Wemmer, D. E. J. Am. Chem. Soc. 1993, 115, 4474.
13. (c) Geierstanger, B. H.; Jacobsen, J. P.; Mrksich, M.; Dervan, P. B.; Wemmer, D. E. Biochemistry 1994, 33, 3055.
14. (a) Mrksich, M.; Dervan, P. B. J. Am. Chem. Soc. 1994, 116, 3663.
15. (b) Chen, Y. H.; Lown, J. W. J. Am. Chem. Soc. 1994, 116, 6995.
16. (a) Mrksich, M.; Parks, M. E.; Dervan, P. B. J. Am. Chem. Soc. 1994, 116, 7983.
17. (b) Parks, M. E.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 6147.
18. (c) Parks, M. E.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 6153.
19. (d) Trauger, J. W.; Baird, E. E.; Dervan, P. B. Chem. Biol. 1996, 3, 369.
20. (e) Swalley, S. E.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 8198.
21. (f) Pilch, D. S.; Pokar, N. A.; Gelfand, C. A.; Law, S. M.; Breslauer, K. J.; Baird, E. E.; Dervan, P. B. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8306.
22. (g) de Claire, R. P. L.; Geierstanger B. H.; Mrksich, M.; Dervan, P. B.; Wemmer, D. E. J. Am. Chem. Soc. In press.
23. Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 6141.
24. (a) Van Dyke, M. W.; Dervan, P. B. Nucl. Acids Res. 1983, 11, 5555.
25. (b) Van Dyke, M. W.; Dervan, P. B. Science 1984, 225, 1122.
26. (a) Taylor, J. S.; Schultz, P. G.; Dervan, P. B. Tetrahedron 1984, 40, 457.
27. (b) Dervan, P. B. Science 1986, 232, 464.
28. (a) Brenowitz, M.; Senear, D. F.; Shea, M. A.; Ackers, G. K. Methods Enzymol. 1986, 130, 132.
29. (b) Brenowitz, M.; Senear, D. F.; Shea, M. A.; Ackers, G. K. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 8462.
30. (c) Senear, D. F.; Brenowitz, M.; Shea, M. A.; Ackers, G. K. Biochemistry 1986, 25, 7344.
31. We note that no conclusion regarding polyamide binding affinities can be drawn from these experiments due to specific and nonspecific interactions of the polyamides with the calf thymus carrier DNA.
32. (a) Trauger, J. W.; Baird, E. E.; Mrksich, M.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 6160.
33. (b) Geierstanger, B. H.; Mrksich M.; Dervan, P. B.; Wemmer, D. E. Nature Struct. Biol. 1996, 3, 321.
34. In support of this, we find that a 12-ring hairpin polyamide motif decreases with regard to both affinity and specificity compared with eight and ten-ring hairpin polyamides.
35. -1) of the polyamide. (See: Barlos, K.; Chatzi, O.; Gatos, D.; Stravropoulos, G.Int. J. Peptide Protein Res. 1991, 37, 513).
36. Sambrook, J.; Fritsch, E. F.; Maniatis, T. Molecular Cloning; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, 1989.
37. (a) Iverson, B. L.; Dervan, P. B. Nucl. Acids Res. 1987, 15, 7823.
38. (b) Maxam, A. M.; Gilbert, W. S. Methods Enzymol. 1980, 65, 499.