Selection of DNA-binding compounds via multistage molecular evolution

Tetrahedron

Volumn 55, Issue 39, 1999, Pages 11687-11697

  Klekota, Bryan ^a   Miller, Benjamin L ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOMYCIN; DNA; IMINE; LIGAND; SERINE PROTEINASE INHIBITOR;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; COMPLEX FORMATION; DNA BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

EID: 0033600898     PISSN: 00404020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0040-4020(99)00687-0     Document Type: Article

References (25)

1. Mullis, K. B.; Faloona, F. A. Methods Enzymol. 1987, 155, 335-350.
2. (a) Szostak, J. W. Trends Biochem. Sci. 1992, 17, 89-93;
3. (b) Tuerk, C.; Gold, L. Science 1990, 249, 505-510.
4. Klekota, B.; Hammond, M. H.; Miller, B. L. Tetrahedron Lett. 1997, 38, 8639-8642.
5. (a) Rowan, S. J.; Hamilton, D. G.; Brady, P. A.; Sanders, J. K. M. J. Am. Chem. Soc. 1997, 119, 2578- 2579;
6. (b) Browan, S. J.; Sanders, J. K. M. J. Org. Chem. 1998, 63, 1536-1546.
7. Hioki, H., Still, W.C. J. Org. Chem. 1998, 63, 904-905.
8. Eliseev, A. V.; Nelen, M. I. J. Am. Chem. Soc. 1997, 119, 1147-1148.
9. Garnovskii, A. D.; Nivorozhkin, A. L.; Minkin, V. I. Coord. Chem. Rev. 1993, 126, 1-69.
10. (a) Gravert, D. J.; Griffin, J. H. J. Org. Chem. 1993, 58, 820-822.
11. (b) Muller, J. G.; Paikoff, S. J.; Rokita, S. E.; Burrows, C. J. J. Inorg. Biochem. 1994, 54, 199-206.
12. (a) Gao, X.; Patel, D. J. Biochemistry 1989, 28, 751-762.
13. (b) Gao, X.; Mirau, P.; Patel, D. J. J. Mol. Biol. 1992, 223, 259-279.
14. (c) Silva, D. J.; Kahne, D. J. Am. Chem. Soc. 1994, 116, 2641-2642.
15. Katz, B. A.; Clark, J. M.; Finer-Moore, J. S.; Jenkins, T. E.; Johnson, C. R.; Ross, M. J.; Luong, C.; Moore, W. R.; Stroud, R. M. Nature 1998, 391, 608-612.
16. (a) Leach, B. E.; Leussing, D. L. J. Am. Chem. Soc. 1971, 93, 3371-3384;
17. (b) McQuate, R. S.; Leussing, D. L. J. Am. Chem. Soc. 1975, 97, 5117-5124;
18. (c) Hopgood, D.; Leussing, D. L. J. Am. Chem. Soc. 1969, 91, 3740-3750.
19. Huc, I., Lehn, J.M. Proc. Natl. Acad. Sci 1997, 94, 2106-2110.
20. This value was derived as follows: considering only tetrahedral coordination, and ignoring symmetry, we have 6 major components (2 amines, salicylaldehyde, 2 imines, and water) to permute. Assuming salicylaldehyde and the two salicylaldimines are the only materials capable of divalent coordination, we have: (1) 2 species coordinated: 6̂4 = 1296 (2) 3 species coordinated: 6̂3 = 216 (3) 2 species coordinated: 3̂2 = 9 which provides a total of 1521 distinct complexes.
21. Good, N. E.; Winget, G. D.; Winter, W.; Connolly, T. N.; Izawa. S.; Singh, R. M. M. Biochemistry 1966, 5, 467-477.
22. Bailar, J. C., Jr.; Emeléus, H. J.; Nyholm, R.; Trotman-Dickernson, A. F., Eds. Comprehensive Inorganic Chemistry 1973, Pergamon Press, Oxford, 1973, vol. 3 p. 238.
23. It is unclear whether the differences in the maximum amount of absorbance observed are significant, or simply a result of experimental error.
24. Of course, since equilibration continues once the library is added to the resin, it is probable that this pre-equilibration step could be eliminated without altering the result.
25. In addition to the measured affinities described in reference (3), we have measured the affinity of the mixture composed of 6, salicylaldehyde, and Zn(2+) for oligo d(A·T) in HEPES/KCI, and found it to be 11 micromolar.