Design of sequence-specific dna binding ligands that use a two-stranded peptide motif for dna sequence recognition

Journal of Biomolecular Structure and Dynamics

Volumn 14, Issue 1, 1996, Pages 31-47

  Nikolaev, V A ^a   Grokhovsky, S L ^a   Surovaya, A N ^a   Leinsoo, T A ^a   Sidonova, N Yu ^a   Zasedatelev, A S ^a   Zhuze, A L ^a   Strahan, G A ^b   Shafer, R H ^b   Gursky, G V ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; POLYPEPTIDE;

ARTICLE; BINDING AFFINITY; BINDING SITE; DNA BINDING; DNA FOOTPRINTING; LIGAND BINDING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DOMAIN;

EID: 9544244880     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1996.10508927     Document Type: Article

References (53)

1. Zimmer, Ch., and Wahnert, U., 1986. Prog. Biophys. Mol. Biol., 47:31–112.
2. Dervan, P. B., 1986. Science, 232:464–471.
3. Zasedatelev, A. S., Gursky, G. V., Zimmer, Ch., and Thrum, H., 1974. Mol. Biol. Rep., 1:337–342.
4. Zasedatelev, A. S., Zhuze, A. L., Zimmer, Ch., Grokhovsky, S. L., Tumanyan, V. G., Gursky, G. V., and Gottikh, B. P., 1976. Dokl. Akad. Nauk USSR, 231:1006–1009.
5. Gursky, G. V., Tumanyan, V. G., Zasedatelev, A. S., Zhuze, A. L., Grokhovsky, S. L., and Gottikh, B. P., 1977. Nucleic Acid-Protein Recognition Edited by:Vogel, H., 189–217. New York:Acad. Press.
6. Krylov, A. S., Grokhovsky, S. L., Zasedatelev, A. S., Zhuze, A. L., Gursky, G. V., and Gottikh, B. P., 1979. Nucleic Acids Res., 6:289–304.
7. Gursky, G. V., Zasedatelev, A. S., Zhuze, A. L., Khorlin, A. A., Grokhovsky, S. L., Streltsov, S. A., Surovaya, A. N., Nikitin, S. M., Krylov, A. S., Retchinsky, V. O., Mikhailov, M. V., Beabealaschvilli, Sh. R., and Gottikh, B. P., 1983. Cold Spring Harbor Symp. Quant. Biol., 47:367–378.
8. Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., and Dickerson, R. E., 1985. Proc. Natl. Acad. Sci. U.S.A., 82:1376–1380.
9. Coll, M., Frederick, C. A., Wang, A. H.-J, and Rich, A., 1987. Proc. Natl. Acad. Sci. U.S.A., 84:8385–8389.
10. Klevit, R. E., Wemmer, D. E., and Reid, B. R., 1986. Biochemistry., 25:3296–3303.
11. Lown, J. W., Krowicki, K., Bhat, U. G., Ward, B., and Dabrowiak, J. C., 1987. Biochemistry, 25:7408–7416.
12. Kissinger, K., Krowicki, K., Dabrowiak, J. C., and Lown, J. W., 1987. Biochemistry, 26:5590–5595.
13. Wade, W. S., and Dervan, P. B., 1987. J. Am. Chem. Soc., 109:1574–1575.
14. Burkhardt, G., Votavova, H., Spooner, J., Luckand, G., and Zimmer, Ch., 1985. J. Biomol. Struct. Dyn., 2:721–736.
15. Pelton, J. G., and Wemmer, D. E., 1989. Proc. Natl. Acad. Sci. U.S.A., 86:5723–5727.
16. Pelton, J. G., and Wemmer, D. E., 1990. J. Am. Chem. Soc., 112:1393–1399.
17. Chen, X., Ramakrishnan, B., Rao, S. T., and Sudaralingam, M., 1994. Struct. Biol., 1:169–175.
18. Wade, W. S., Mrksich, M., and Dervan, P. B., 1992. J Am. Chem. Soc., 114:8783–8792.
19. Mrksich, M., Wade, W. S., Dwyer, T. J., Geierstanger, B. H., Wemmer, D. E., and Dervan, P. B., 992. Proc. Natl. Acad. Sci. U.S.A., 89:7586–7590.
20. Dwyer, T., Geierstanger, B. H., Bathini, Y., Lown, J. W., and Wemmer, D. E., 1992. J. Am. Chem. Soc., 114:5911–5919.
21. Geierstanger, B. H., Dwyer, T., Bathini, Y., Lown, J. W., and Wemmer, D. E., 1993. J. Am. Chem. Soc., 115:4474–4482.
22. Geierstanger, B. H., Mrksich, M., Dervan, P. B., and Wemmer, D. E., 1994. Science, 266:646–650.
23. Waring, M. J., and Fox, K. R., 1983. Molecular Aspects of Anticancer Drug Action Edited by:Neidle, S., and Waring, M. J., 127–156. Verlag Chemie
24. Wang, A.M.-J, Ughetto, G. J., Quigley, T., Hakoshima, T., van der Marel, G. A., van Boom, J. H., and Rich, A., 1984. Science., 225:1115–1123.
25. Addess, K. J., Sinsheimer, J. C., and Feigen, J., 1993. Biochemistry, 23:2496–2508.
26. A Streltsov, S., Khorlin, A. A., Surovaya, A. N, Gursky, G. V., Zasedatelev, A. S, Zhuze, A. L., and Gottikh, B. P., 1980. Biofizika (USSR), 25:929–941.
27. Yu Vengerov, Yu., Semenov, T. E., Surovaya, A. N, Sidorova, N. Yu., Streltsov, S. A., Khorlin, A. A., Zhuze, A. L., and Gursky, G. V., 1988. J. Biomol. Struct. Dyn., 6:311–330.
28. Grokhovsky, S. L., Surovaya, A. N., Sidorova, Yu. N., Votavova, H., Sponar, J., Frich, I., and Gursky, G. V., 1988. Mol.Biol., 22:1315–1333.
29. Sidorova, N. Yu., Surovaya, A. N., Nikolaev, V. A., Zhuze, A. L, and Gursky, G. V., 1991. Mol. Biol., 25:706–717.
30. A Leinsoo, T., Nikolayev, V. A., Grokhovsky, S. L., Streltsov, S. A., Zasedatelev, A. S., Zhuze, A. L., and Gursky, G. V., 1988. Mol.Biol., 22:159–179.
31. Leinsoo, T. A., Nikolaev, V. A., Grokhovsky, S. L., Surovaya, A. N., Sidorova, Yu. N., Streltsov, S. A., Zasedatelev, A. S., Zhuze, A. L, and Gursky, G. V. 1989. Mol. Biol., 23:1616–1637.
32. Ovchinnikov, Yu. A., Guryev, S. O., Krayev, A. S., Monastyrskaya, G. S, Skryabin, K. G., Sverdlov, E. D., Zhakaryev, V. M., and Bayev, A. A., 1979. Gene, 6:235–249.
33. Sambrook, J., Fritsch, E. F, and Maniatis, T., 1989. Molecular Cloning. A Laboratory Manual, 2nd ed. New York:Cold Spring Harbour Laboratory, Cold Spring Harbor.
34. Jacobs, P., Cravador, A., Loriau, R., Brockly, F., Colau, B., Chuchana, P., Von Elsen, A., Herzog, A., and Bollen, A., 1985. DNA, 4:139–146.
35. Galas, D. J., and Schmitz, A., 1976. Nucleic Acids Res., 5:3157–3170.
36. Maxam, A. M., and Gilbert, W., 1980. Methods in Enzymology, 65:499–560.
37. Ulyanov, N. B., Gorin, A. A., and Zhurkin, V. B., 1989. Proceedings of the International Conference on Supercomputing 89:Supercomputer Applications Edited by:Kaitashev, L. P., and Kartashev, S. L., 368–370. St. Petersburg, FL:International Supercomputing Institute Inc.
38. Zhurkin, V. B., Gorin, A. A, Charakhchyan, A. A., and Ulyanov, N. B., 1990. Theoretical Biochemistry and Molecular Biophysics Edited by:Beveridge, D. L., and Lavery, R., 409–429. New York:Adenine Press.
39. Tabernero, L., Verdaguer, N., Coll, M., Fita, I., Van Der Marel, G. A., Van Boom, J. H., Rich, A., and Aymami, J., 1993. Biochemistry, 32:8403
40. Addess, K. J., and Feigon, J., 1994. Biochemistry, 33:12386–12396.
41. Stewart, J. J.P., 1990. J. Computer-Aided Molec. Design, 4:1–105.
42. Cornell, W. D., Cieplak, P., Bayly, C. L., Gould, I. R., Merz, Ir., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179–5197.
43. Pearlman, D. A., Case, D. A., Caldell, J. W., Ross, W. S., III, Cheatham, T. E., Ferguson, D. M., Seibel, G. L, Singh, U. C., Weiner, P. K, and Kollman, P. A., 1995. AMBER Vol. 41, San Francisco:University of California.
44. Gallo, K., Huang, C., Ferrin, T. E., and Landgridge, R., 1989. Molecular Interactive Display and Simulation San Francisco:(MLDASplus), University of California.
45. Kozman, L. I., Gause, G. G., Galkin, V. L., and Dudnik, Yu. V., 1978. Antibiotics, 23:602–606.
46. Petrusek, R. L., Anderson, G. L., Gamer, T. F., Fannin, O. L., Kaplan, D. J., Zimmer, S. G, and Hurley, L. H., 1981. Biochemistry., 20:111 1–1119
47. Graves, D. E., Stone, M. P., and Krugh, T. R., 1985. Biochemistry, 24:7573–7581.
48. Gursky, G. V., and Zasedatelev, A. S., 1984. Sov. Sci. Rev. D. Physico-Chem. Biol., 5:53–139.
49. Gursky, G. V., Grokhovsky, S. L., Nikolaev, V. A., Surovaya, A. N., Chernov, B. K., Pismensky, V. F., Sidorova, Yu. N., Zasedatelev, A. S., Zhuze, A. L, and Shafer, R. H., 1995. J. Biomol., Str. Dyn. 12, a081
50. Gursky, G. V., Tumanyan, V. G., Zasedatelev, A. S., Zhuze, A. L., Grokhovsky, S. L, and Gottikh, B. P., 1976. Mol.Biol. Reports, 2:413–425.
51. Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B., 1993. Nature, 365:512–520.
52. Kim, J. L., Nikolov, D. B., and Burley, S. K., 1993. Nature, 365:520–527.
53. Church, G. M., Sussman, I. L., and Kim, S-. H., 1977. Proc. Nat. Acad. Sci. U.S.A., 74:1458–1462.