How different DNA-binding proteins affect long-range oxidative damage to DNA

Biochemistry

Volumn 40, Issue 18, 2001, Pages 5556-5564

  Rajski, Scott R ^a   Barton, Jacqueline K ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OXIDATIVE DAMAGE;

BINDING ENERGY; DNA; ELECTRIC CHARGE; ENZYMES; MODULATION; PACKING; PHOTOOXIDATION; TRANSPORT PROPERTIES;

BIOCHEMISTRY;

DNA BASE; DNA BINDING PROTEIN; HOMEODOMAIN PROTEIN; METHYLTRANSFERASE; RESTRICTION ENDONUCLEASE; RHODIUM; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BASE PAIRING; BINDING SITE; DNA BINDING; DNA DAMAGE; ELECTRON TRANSPORT; MOLECULAR INTERACTION; OXIDATIVE STRESS; PHOTOOXIDATION; PRIORITY JOURNAL; PROTEIN DNA BINDING;

ANTENNAPEDIA HOMEODOMAIN PROTEIN; BASE PAIR MISMATCH; BINDING SITES; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; DNA DAMAGE; DNA-BINDING PROTEINS; HOMEODOMAIN PROTEINS; INTERCALATING AGENTS; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; OXIDANTS, PHOTOCHEMICAL; RECOMBINANT PROTEINS; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS;

EID: 0035826678     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi002684t     Document Type: Article

References (59)

1. Kelley, S. O., and Barton, J. K. (1999) Met. Ions Biol. Syst. 36, 211-249;
2. (b) Rajski, S. R., Jackson, B., and Barton, J. K. (2000) Mutat. Res. 447, 49-72;
3. (c) Schuster, G. B. (2000) Acc. Chem. Res. 33, 253-260;
4. (d) Geise, B. (2000) Acc. Chem. Res. 33, 631-636.
5. (a) Núñez, M. E., Hall, D. B., and Barton, J. K. (1999) Chem. Biol. 6, 85-97;
6. (b) Ly, D., Sanii, L., and Schuster, G. B. (1999) J. Am. Chem. Soc. 121, 9400-9410.
7. (a) Williams, T. T., Odom, D. T., and Barton, J. K. (2000) J. Am. Chem. Soc. 122, 9048-9049;
8. (b) Kelley, S. O., Holmlin, R. E., Stemp, E. D. A., and Barton, J. K. (1997) J. Am. Chem. Soc. 119, 9861-9870;
9. (c) Hall, D. B., and Barton, J. K. (1997) J. Am. Chem. Soc. 119, 5045-5046.
10. (a) Sugiyama, H., and Saito, I. (1996) J. Am. Chem. Soc. 118, 7063-7068;
11. (b) Saito, I., Nakamura, T., Nakatani, K., Yoshioka, Y., Yamaguchi, K., and Sugiyama, H. (1998) J. Am. Chem. Soc. 120, 12686-12687;
12. (c) Sugiyama, H., and Saito, I. (1996) J. Am. Chem. Soc. 118, 7063-7068.
13. Prat, F., Houk, K. N., and Foote, C. S. (1998) J. Am. Chem. Soc. 120, 845.
14. Hall, D. B., Holmlin, R. E., and Barton, J. K. (1996) Nature 382, 731-735.
15. Arkin, M. R., Stemp, E. D. A., Pulver, S. C., and Barton, J. K. (1997) Chem. Biol. 4, 389-400.
16. (a) Gasper, S. M., and Schuster, G. B. (1997) J. Am. Chem. Soc. 119, 12762-12771;
17. (b) Henderson, P. T., Jones, D., Hampikian, G., Kan, Y., and Schuster, G. B. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 8353-8358;
18. (c) Ly, D., Sanii, L., and Schuster, G. B. (1999) J. Am. Chem. Soc. 121, 9400-9410;
19. (d) Kan, Y., and Schuster, G. B. (1999) J. Am. Chem. Soc. 121, 10857-10864;
20. (e) Sartor, V., Henderson, P. T., and Schuster, G. B. (1999) J. Am. Chem. Soc. 121, 11027-11032.
21. (a) Meggers, E., Michel-Beyerle, M. E., and Giese, B. (1998) J. Am. Chem. Soc. 120, 12950-12955;
22. (b) Giese, B., Wessely, M., Spormann, M., Lindermann, U., Meggers, E., and Michel-Beyerle, M. E. (1999) Angew. Chem., Int. Ed. Engl. 38, 996-998;
23. (c) Meggers, E., Kusch, D., Spichty, M., Wille, U., and Giese, B. (1998) Angew. Chem., Int. Ed. Engl. 37, 460-462.
24. (a) Nakatani, K., Dohno, C., and Saito, I. (1999) J. Am. Chem. Soc. 121, 10854-10855;
25. (b) Nakatani, K., Dohno, C., and Saito, I. (1999) J. Org. Chem. 64, 6901-6904.
26. Hall, D. B., Kelley, S. O., and Barton, J. K. (1998) Biochemistry 37, 15933-15940.
27. Núñez, M. E., Noyes, K. T., Gianolio, D. A., McLaughlin, L. W., and Barton, J. K. (2000) Biochemistry 39, 6190-6199.
28. Rajski, S. R., Kumar, S., Roberts, R. J., and Barton, J. K. (1999) J. Am. Chem. Soc. 121, 5615-5616.
29. (a) Cheng, X., Kumar, S., Posfai, J., Pflugrath, J. W., and Roberts, R. J. (1993) Cell 74, 299-307;
30. (b) O'Gara, M., Klimasauskas, S., Roberts, R. J., and Cheng, X. (1996) J. Mol. Biol. 261, 634-645.
31. (a) Mi, S., Alonso, D., and Roberts, R. J. (1995) Nucleic Acids Res. 23, 620-627;
32. (b) Garcia, R. A., Bustamante, C. J., and Reich, N. O. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 7618-7622.
33. Wagenknecht, H. A., Rajski, S. R., Pascaly, M., Stemp, E. D. A., and Barton, J. K. (2001) J. Am. Chem. Soc., in press.
34. (a) Beaucage, S. L., and Caruthers, M. H. (1981) Tetrahedron Lett. 22, 1859-1802;
35. (b) Caruthers, M., Beaton, G., Wu, J. V., and Wiesler, W. (1992) Methods Enzymol. 211, 3-20;
36. (c) Goodchild, J. (1990) Bioconjugate Chem. 1, 165-187.
37. Holmlin, R. E., Dandliker, P. J., and Barton, J. K. (1999) Bioconjugate Chem. 10, 1122-1130.
38. Klimasauskas, S., and Roberts, R. J. (1995) Nucleic Acids Res. 23, 1388-1395.
39. O'Gara, M., Horton, J. R., Roberts, R. J., and Cheng, X. (1998) Nat. Struct. Biol. 5, 872-877.
40. A closely related analogue of 4-Mel has recently been shown to be well stacked within duplex DNA when paired with a complementary non-hydrogen bonding base. See: Guckian, K. M., Krugh, T. R., and Kool, E. T. (2000) J. Am. Chem. Soc. 122, 6841-6847.
41. (a) De Souza, O. N., and Ornstein, R. L. (1998) Biopolymers 46, 403-415;
42. (b) Coleman, R. A., Taggart, A. K. P., Benjamin, L. R., and Pugh, B. F. (1995) J. Biol. Chem. 270, 13842-13849;
43. (c) Lee, D. K., Horikoshi, M., and Roeder, R. G. (1991) Cell 67, 1241-1250.
44. (a) Kim, J. L., Nikolov, D. B., and Burley, S. K. (1993) Nature 365, 520-527;
45. (b) Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993) Nature 365, 512-520.
46. (a) Meggers, E., Michel-Beyerle, M. E., and Giese, B. (1998) J. Am. Chem. Soc. 120, 12950-12955;
47. (b) Nakatani, K., Dohno, C., and Saito, I. (2000) J. Am. Chem. Soc. 122, 5893-5894.
48. Cheng, X., Balendiran, K., Schildkraut, I., and Anderson, J. E. (1994) EMBO J. 13, 3927-3935.
49. (a) LeRoux, I., Joliot, A. H., Bloch-Gallego, E., and Prochiantz, A. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 9120-9124;
50. (b) Derossi, D., Calvet, S., Trembleau, A., Brunissen, A., Chassaing, G., and Prochiantz, A. (1996) J. Biol. Chem. 271, 18188-18193;
51. (c) Affolter, M., Percival-Smith, A., Martin, Muller, M., Leupin, W., and Gehring, W. J. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4093-4097;
52. (d) Derossi, D., Joliot, A. H., Chassaing, G., and Prochiantz, A. (1994) J. Biol. Chem. 269, 10444-10450.
53. (a) Fraenkel, E., and Pabo, C. O. (1998) Nat. Struct. Biol. 5, 692-697;
54. (b) Billeter, M., et al. (1993) J. Mol. Biol. 234, 1084-1093;
55. (c) Billeter, M., Guntert, P., Luginbuhl, P., and Wuthrich, K. (1996) Cell 85, 1057-1065.
56. (a) Fiebig, T., Wan, C. Z., Kelley, S. O., Barton, J. K., and Zewail, A. H. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 1187-1192;
57. (b) Wan, C. Z., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K., and Zewail, A. H. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 6014-6019.
58. Odom, D. T., Dill, E. A., and Barton, J. K. (2000) Chem. Biol. 7, 475-481.
59. Núñez, M. E., Rajski, S. R., and Barton, J. K. (2000) Methods Enzymol. 319, 165-188.