DNA Recognition by Structure-Selective Nucleases

Biopolymers - Biospectroscopy Section

Volumn 44, Issue 4, 1997, Pages 405-421

  Suck, Dietrich ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

5 nucleases; DNA recognition; DNase 1; P1 and S1 nucleases; Structure selective nucleuses; T4 endonuclease VII; X ray structure

Indexed keywords

BACTERIA (MICROORGANISMS); EUKARYOTA;

CONFORMATIONS; DNA; ENZYMES; X RAY DIFFRACTION ANALYSIS;

DNA RECOGNITION; NUCLEASES; STRUCTURAL SELECTIVITY;

DNA SEQUENCES;

DNA; NUCLEASE;

BINDING SITE; ENZYME BINDING; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PROTEIN DNA BINDING; REVIEW;

BINDING SITES; CATALYTIC DOMAIN; DNA; DNA, SINGLE-STRANDED; ENDODEOXYRIBONUCLEASES; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY;

EID: 0031224812     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(1997)44:4<405::aid-bip5>3.0.co;2-l     Document Type: Article

References (88)

1. Volbeda, A., Lahm, A., Sakiyama, F. & Suck, D. (1991) EMBO J. 10, 1607-1618.
2. Törö, I., Kitamoto, K. & Suck, D. (1998) in preparation.
3. Suck, D. (1994) J. Mol. Recogn. 7, 65-70.
4. Mol, C. D., Kuo, C-F., Thayer, M. M., Cunningham, R. P. & Tainer, J. A. (1995) Nature 374, 381-386.
5. Gorman, M. A., Morera, S., Rothwell, D. G., de la Fortelle, E., Mol, C. D., Tainer, J. A., Hickson, I. D. & Freemomt, P. S. (1997) EMBO J. 16, 6548-6558.
6. Ceska, T. A., Sayers, J. R., Stier, G. & Suck, D. (1996) Nature 382, 90-93.
7. Mueser, T. C., Nossal, N. G. & Hyde, C. C. (1996) Cell 85, 1101-1112.
8. Kim, Y., Eom, S. H., Wang, J., Lee, D.-S., Suh, S. W. & Steitz, T. A. (1995) Nature 376, 612-616.
9. Raaijmakers, H., Vix. O., Törö, I., Golz, S., Kemper, B. & Suck, D. (1998) in preparation.
10. Ariyoshi, M., Vassylyev, D. G., Iwasaki. H., Nakamura, H. Shinagawa, H. & Morikawa, K. (1994) Cell 78, 1063-1072.
11. Vassylyev, D. G., Kashiwagi, T., Mikami, Y., Ariyoshi, M., Iwai, S., Ohtsuka, E. & Morikawa, K. (1995) Cell 83, 773-783.
12. Lloyd, R. S. & Cheng, X. (1997) Biopolymers Nucleic Acid Sci. 44, 139-149.
13. Seeman, N. C., Rosenberg, J. M. & Rich. A. (1976) Proc. Natl. Acad. USA 73, 804-808.
14. Pavletich, N. P. & Pabo, C. O. (1991) Science 252, 809-817.
15. Harrison, S. C. & Aggarwal, A. K. (1990) Ann. Rev. Biochem. 59, 933-969.
16. Steitz, T. A. (1990) Quart. Rev. Biophys. 23, 205-280.
17. Pabo, C. O. & Sauer, R. T. (1992) Ann. Rev: Biochem. 61, 1053-1095.
18. Lesser, D. R., Kurpiewski, M. R. & Jen-Jacobson, L. (1990) Science 250, 776-786.
19. Jen-Jacobson, L. (1997) Biopolymers Nucleic Acid Sci. 44, 153-180.
20. Hol, W. G. J. (1985) Progr. Biophys. Mol. Bial. 45, 149-195.
21. Kim, Y. C., Grable, J. C., Love, R., Greene, P. J. & Rosenberg, J. M. (1990) Science 249, 1307-1309.
22. Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I. & Aggarwal, A. K. (1994) Nature 368, 660-664.
23. Suck, D. (1997) Nature Struct. Biol. 4, 161-165.
24. Kim, Y., Geiger, J. H., Hahn, S. & Sigler, P. B. (1993) Nature 365, 512-520.
25. Kim, J. L., Nikolov, D.B. & Burley, S. K. (1993) Nature 365, 520-527.
26. Robinson, H., Gao, Y.-G., McCrary, B. S., Edmondson, S. P., Shriver, J. W. & Wang, A. H.-J. (1998) Nature 392, 202-205.
27. Suck, D. (1992) in Molecular Structure and Life, Kyogoku, Y. & Nishimura, Y., Eds., CRC Press, Boca Raton, FL, pp. 141-156.
28. Shishido, K. & Ando, T. (1982) in Nucleuses, Linn, S. M. & Roberts, R. J., Eds., Cold Spring Harbor Laboratory Press, New York, pp. 155-185.
29. Fujimoto, M., Kuninaka, A. & Yoshino, H. (1974) Agr. Biol. Chem. 38, 1555-1561.
30. Vogt, V. M. (1973) Eur. J. Biochem. 33, 192-200.
31. Fujimoto, M., Fujiyama, K., Kuninaka, A. & Yoshino, H. (1974) Agr. Biol. Chem. 38, 2141-2147.
32. Box, H. C., Budzinski, E. E., Evans, M. S., French, J. B. & Maccubin, A. E. (1990) Biochim. Biophys. Acta 1161, 291-294.
33. Weinfeld, M., Liuzzi, M., & Paterson, M. C. (1989) Nucleic Acids Res. 17, 3735-3745.
34. Weinfeld, M., Soderlind, K. J. M. & Buchko, G. W. (1993) Nucleic Acids Res. 21, 621-626.
35. Romier, C., Dominguez, R., Lahm, A., Dahl, O. & Suck, D. (1998) Protein Struct. Funct. Genet., in press.
36. Vogt, V. M. (1980) Methods Enzymol. 65, 248-255.
37. Hough, E., Hansen, L. K., Birknes, B., Jynge, K., Hansen, S., Hordvik, A., Little, C., Dodson, E. & Derewenda, Z. (1989) Nature 338, 357-360.
38. Nagai, K. (1996) Curr. Opin. Struct. Biol. 6, 53-61.
39. Suck, D. (1997) Nature Struct. Biol. 4, 161-165.
40. Bochkarev, A., Pfuetzner, R. A., Edwards, A. M. & Frappier, L. (1997) Nature 385, 176-181.
41. Beese, L. S. & Steitz, T. A. (1991) EMBO J. 10, 25-33.
42. Wang, J., Yu, P., Lin, T. C., Konigsberg, W. H. & Steitz, T. A. (1996) Biochemistry 35, 8110-8119.
43. Drew, H. R. & Travers, A. A. (1984) Cell 37, 491-502.
44. Lahm, A., Weston, S. A. & Suck, D. (1991) Nucleic Acids Mol. Biol. 5, 172-186.
45. Hochschild, A. & Ptashne, M. (1986) Cell 44, 681-687.
46. Hogan, M. E., Roberson, M.W. & Austin, R. H. (1989) Proc. Natl. Acad. Sci. USA 86, 9273-9277.
47. Brukner, I., Sanchez, R., Suck, D. & Pongor, S. (1995) EMBO J. 14, 1812-1818.
48. Oefner, C. & Suck, D. (1986) J. Mol. Biol. 192, 605-632.
49. Suck, D., Lahm, A. & Oefner, C. (1988) Nature 332, 465-468.
50. Lahm, A. & Suck, D. (1991) J. Mol. Biol. 222, 645-667.
51. Weston, S., Lahm, A. & Suck, D. (1992) J. Mol. Biol. 226, 1237-1256.
52. Weston, S. & Suck, D. (1993) Protein Eng. 6, 349-357.
53. Doherty, A. J., Worrall, A. F. & Connolly, B. A. (1995) J. Mol. Biol. 251, 366-377.
54. Wolf, E., Brukner, I. & Suck, D. (1995) Protein Eng. 8, 283-291.
55. Barzilay, G., Mol, C. D., Robson, C. N., Walker, L. J., Cunningham, R. P., Tainer, J. A. & Hickson, I. D. (1995) Nature Struct. Biol. 2, 561-567.
56. Barzilay, G. & Hickson, I. D. (1995) Bioessays 17, 713-719.
57. Feng, Q., Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916.
58. Matsuo, Y., Yamada, A., Tsukamoto, K., Tamura, H.-O., Ikezawa, H., Nakamura, H. & K. (1996) Protein Sci. 5, 2459-2467.
59. Smith, J. L., Zaluzek, E. J., Wery, J.-P., Nin, L., Switzer, R. L., Zalkin, H. & Satow, Y. (1994) Science 264, 1427-1433.
60. Kornberg, A. & Baker, T. (1992) DNA Replication. 2nd ed., W. H. Freeman, New York.
61. Lieber, M. R. (1997) BioEssays 19, 233-240.
62. Harrington, J. J. & Lieber, M. R. (1994) EMBO J. 13, 1235-1246.
63. Lyamichev, V., Brow, M. A. D. & Dahlberg, J. E. (1993) Science 260, 778-783.
64. Bhagwat, M., Hobbs, L. J. & Nossal, N. J. (1997) J. Biol. Chem. 272, 28523-28530.
65. Gutman, P.D. & Minton, K. W. (1993) Nucleic Acids Res. 21, 4406-4407.
66. Murante, R. S., Rust, L. & Bambara, R. A. (1995) J. Biol. Chem. 270, 30377-30383.
67. Garforth, S. J., Ceska, T. A., Suck, D. & Sayers, J. R. (1998) in preparation.
68. Artymiuk, P. J., Ceska, T. A., Suck, D. & Sayers, J. R. (1997) Nucleic Acids Res. 25, 4224-4229.
69. West, S. C. (1993) in Nucleases, 2nd ed., Linn, S. M., Lloyd, R. S. & Roberts, R. J., Eds., Cold Spring Harbor Laboratory Press, New York, pp. 145-170.
70. Kemper, B. (1997) in DNA Damage and Repair, Vol. 1: DNA Repair in Prokaryotes and Lower Eukaryotes, Nickoloff, J. A. & Hoekstra, M. F., Eds., Humana Press Inc., Totowa, NJ, pp. 179-204.
71. White, M. F., Giruad-Panis, M-J., Pöhler, J. R. G. & Lilley, D. M. J. (1997) J. Mol. Biol. 269, 647-664.
72. Mizuuchi, K., Kemper, B., Hays, J. & Weisberg, R. A. (1982) Cell 29, 357-365.
73. Grebenshchikova, S. M. L., Plugina, L. A. & Shcherbakov, V. P. (1994) Genetika 30, 622-626.
74. Kemper, B. & Brown, D. T. (1976) J. Viral. 18, 1000-1015.
75. Kemper, B., Pottmeyer, S., Solaro, P. & Kosak, H. (1990) in Structure and Methods, Vol. 1. Human Genome Initiative and DNA Recombination, Sarma. R. H. & Sarma, M. H., Eds., Adenine Press, Schenectady, NY, pp. 215-229.
76. Bhattacharyya, A. A., Murchie, A. I. H., v. Kitzing, E., Diekmann, S., Kemper, B. & Lilley, D. M. J. (1991) J. Mol. Biol. 221, 1191-1207.
77. Lilley, D. M. J. & Clegg, R. M. (1993) Quart. Rev. Biophys. 26, 131-175.
78. Youil, R., Kemper, B. & Cotton, R. G. H. (1995) Proc. Natl. Acad. Sci. USA 92, 87-91.
79. Giraud-Panis, M.-J. E. & Lilley, D. M. J. (1997) EMBO J. 16, 2528-2534.
80. Solaro, P. C., Birkenkamp, K., Pfeiffer, P. & Kemper, B. (1993) J. Mol. Biol. 230, 868-877.
81. Pottmeyer, S. & Kemper, B. (1992) J. Mol. Biol. 223, 607-615.
82. Schofield, M. J., Lilley, D. M. J. & White, M. F. (1998) Biochemistry 37, 7733-7740.
83. Giraud-Panis, M.-J. E., Duckett, D. R. & Lilley, D. M. J. (1995) J. Mol. Biol. 252, 596-610.
84. Golz, S., Christoph, A., Birkenkamp-Demtröder & Kemper, B. (1997) Eur. J. Biochem. 245, 573-580.
85. Giraud-Panis, M.-J. E. & Lilley, D. M. J. (1996) J. Biol. Chem. 271, 33148-33155.
86. Von Kitzing, E., Lilley, D. M. J. & Diekmann, S. (1990) Nucleic Acids Res. 18, 2671-2683.
87. Iwasaki, H., Takahagi, M., Nakata, A. & Shinagawa, H. (1991) EMBO J. 10, 4381-4389.
88. Bennet, R. J. & West, S. C. (1995) Proc. Natl. Acad. Sci. USA 92, 5635-5639.