Programmable oligomers for minor groove DNA recognition

Journal of the American Chemical Society

Volumn 128, Issue 28, 2006, Pages 9074-9079

  Doss, Raymond M ^a   Marques, Michael A ^a   Foister, Shane ^a   Chenoweth, David M ^a   Dervan, Peter B ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; CATALYST SELECTIVITY; CATALYSTS; MOLECULAR STRUCTURE; OLIGOMERS;

AROMATIC CARBOXAMIDES; DISTAMYCIN; GROOVE RECOGNIZATION; PROGRAMMABLE OLIGOMERS;

DNA;

BIOMIMETIC MATERIAL; CHLOROTHIOPHENE DERIVATIVE; DEOXYRIBONUCLEASE I; DIMER; DISTAMYCIN A; DNA; HETEROCYCLIC COMPOUND; HYDROXYBENZIMIDAZOLE DERIVATIVE; HYDROXYPYRROLE DERIVATIVE; IMIDAZOLE DERIVATIVE; IMIDAZOPYRIDINE DERIVATIVE; IMIDAZOPYRROLE DERIVATIVE; OLIGOMER; OXAZOLE DERIVATIVE; POLYAMIDE; PYRROLE DERIVATIVE; THIOPHENE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; BINDING AFFINITY; CONFORMATIONAL TRANSITION; DNA BINDING; DNA FOOTPRINTING; HYDROGEN BOND; MOLECULAR RECOGNITION; POLYMERASE CHAIN REACTION; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SYNTHESIS;

BASE PAIRING; DNA; NUCLEIC ACID CONFORMATION; NYLONS; OLIGONUCLEOTIDES; PROTEIN BINDING; PYRROLES;

EID: 33746034937     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0621795     Document Type: Article

References (39)

1. (a) Darnell, J. E. Nat. Rev. Cancer 2002, 2, 740-748.
2. (b) Pandolfi, P. P. Oncogene 2001, 20, 3116-3127.
3. (c) Dervan, P. B.; Edelson, B. S. Curr. Opin. Struct. Biol. 2003, 13, 284-299.
4. (a) Finlay, A. C.; Hochstein, F. A.; Sobin, B. A.; Murphy, F. X. J. Am. Chem. Soc. 1951, 73, 341-343.
5. (b) Arcamone, F. N. V.; Penco, S.; Orczzi, P.; Nicolella, V.; Pirelli, A. Nature 1964, 203, 1064-1065.
6. (a) Kopka, M. L.; Yoon, C.; Goodsell, D.; Pjura, P.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 1376-1380.
7. (b) Pelton, J. G.; Wemmer, D. E. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5723-5727.
8. (c) Wemmer, D. E. Annu. Rev. Biomol. Struct. 2000, 29, 439-461.
9. (d) Buchmueller, K. L.; Staples, A. M.; Howard, C. M.; Horick, S. M.; Uthe, P. B.; Minh Le, N.; Cox, K. K.; Nguyen, B.; Pacheco, K. A. O.; Wilson, D. W.; Lee, M. J. Am. Chem. Soc. 2004, 127, 742-750.
10. (e) Baraldi, P. G.; Bovero, A.; Fruttarolo, F.; Preti, D.; Tabrizi, M. A.; Pavani, M. G.; Romagnoli, R. Med. Res. Rev. 2004, 24, 475-528.
11. (f) Reddy, P. M.; Toporowski, J. W.; Kahane, A. L.; Bruice, T. C. Bioorg. Med. Chem. Lett. 2005, 15, 5531-5536.
12. White, S.; Szewczyk, J. W.; Turner, J. M.; Baird, E. E.; Dervan, P. B. Nature 1998, 391, 468-471.
13. (a) Kielkopf, C. L.; White, S.; Szewcyzk, J. W.; Turner, J. M.; Baird, E. E.; Dervan, P. B.; Rees, D. C. Science 1998, 282, 111-115.
14. (b) Kielkopf, C. L.; Bremer, R. E.; White, S.; Szewczyk, J. W.; Turner, J. M.; Baird, E. E.; Dervan, P. B.; Rees, D. C. J. Mol. Biol. 2000, 295, 557-567.
15. (a) Urbach, A. R.; Szewczyk, J. W.; White, S.; Turner, J. M.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Sac. 1999, 121, 11621-11629.
16. (b) White, S.; Turner, J. M.; Szewezyk, J. W.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1999, 121, 260-261.
17. (a) Hays, F. A.; Teegarden, A.; Jones, Z. J. R.; Harms, M.; Raup, D.; Watson, J.; Cavaliere, E.; Shing Ho, P. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7157-7162.
18. (b) Beveridge, D. L.; Barreiro, G.; Byun, K. S.; Case, D. A.; Cheatham, T. E., 3rd; Dixit, S. B.; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Seibert, E.; Sklenar, H.; Stoll, G.; Thayer, K. M.; Varnai, P.; Young, M. A. Biophys. J. 2004, 87, 3799-3813.
19. (c) Dixit, S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E., 3rd; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Biophys. J. 2005, 89, 3721-3740.
20. (d) Wu, H.; Crothers, D. M. Nature 1984, 308, 509.
21. (e) Steitz, T. A. Annu. Rev. Biophys. 1990, 23, 205.
22. (f) Goodsell, D. S.; Kopka, M. L.; Cascio, D.; Dickerson, R. E. Proc. Natl. Sci. U.S.A. 1993, 90, 2930.
23. (g) Paolella, D. N.; Palmer, R.; Schepartz, A. Science 1994, 264, 1130.
24. (h) Kahn, J. D.; Yun, E.; Crothers. D. M. Nature 1994, 368 163.
25. (i) Geierstanger, B. H.; Wemmer, D. E. Annu. Rev. Biochem. 1995, 24, 463.
26. (j) Hansen, M. R.; Hurley, L. H. Acc. Chem. Res. 1996, 29, 249.
27. (k) Turner, J. M.; Swalley, S. E.; Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1998, 120, 6219-6226.
28. (l) Marques, M. A.; Doss, R. M.; Urbach, A. R.; Dervan, P. B. Helv. Chim. Acta 2002, 85, 4485-4517.
29. Foister, S.; Marques, M. A.; Doss, R. M.; Dervan, P. B. Bioorg. Med. Chem. 2003, 11, 4333-4340.
30. Briehn, C. A.; Weyermann, P.; Dervan, P. B. Chem.-Eur. J. 2003, 9, 2110-2122.
31. (a) Renneberg, D.; Dervan, P. B. J. Am. Chem. Soc. 2003, 125, 5707-5716.
32. (b) Marques, M. A.; Doss, R. M.; Foister, S.; Dervan, P. B. J. Am. Chem. Soc. 2004, 126, 10339-10349.
33. For downregulation of an endogenous gene in cell culture by polyamides see: Olenyuk, B. Z.; Zhang, G.; Klco, J. M.; Nickols, N. G.; Kaelin, W. G., Jr.; Dervan, P. B. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16768-16773.
34. Heterocycle pair refers to cofacial stack (noncovalent interaction), whereas dimer refers to two covalently attached heterocycles.
35. Baird, E. E.; Dervan, P. B. J. Am. Chem. Soc. 1996, 118, 6141-6146.
36. Urbach, A. R.; Dervan, P. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4343-4348.
37. Trauger, J. W.; Dervan, P. B. J. Methods Enzymol. 2001, 340, 450-466.
38. -1 where W = A or T (see ref 10b).
39. Urbach, A. R.; Love, J. J.; Ross, S. A.; Dervan, P. B. J. Mol. Biol. 2002, 320, 55-71.