The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch

Acta Crystallographica Section D: Biological Crystallography

Volumn 63, Issue 6, 2007, Pages 673-681

  Kondo, Jiro ^a,b   Sunami, Tomoko ^a   Takénaka, Akio ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Base intercalated duplex; Intra duplex and inter duplex hand in pocket motifs; Single stranded DNA

Indexed keywords

DEOXYRIBONUCLEOTIDE;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; HUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEOTIDES; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; POINT MUTATION;

EID: 34249109338     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444907012607     Document Type: Article

References (72)

1. Armour, J. A., Wong, Z., Wilson, V., Royle, N. J. & Jeffreys, A. J. (1989). Nucleic Acids Res. 17, 4925-4935.
2. Baeyens, K. J., De Bondt, H. L., Pardi, A. & Holbrock, S. R. (1996). Proc. Natl Acad. Sci. USA, 93, 12851-12855.
3. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. (2000). Science, 289, 905-920.
4. Baugh, C., Grate, D. & Wilson, C. (2000). J. Mol. Biol. 301, 117-128.
5. Berglund, J. A., Rosbash, M. & Schultz, S. C. (2001). RNA, 7, 682-691.
6. Brünger, A. T. (1992). Nature (London), 355, 472-475.
7. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
8. Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T. & Ramakrishnan, V. (2000). Nature (London), 407, 340-348.
9. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R. & Doudna, J. A. (1996). Science, 273, 1678-1685.
10. Chou, S.-H. & Chin, K. H. (2001). J. Mol. Biol. 314, 139-152.
11. Collaborative Computational Project, Number 4 (1994) Acta Cryst. D50, 760-763.
12. De Luca, F., Reyes, A., Veronico, P., Di Vito, M., Lamberti, F. & De Giorgi, C. (2002). Gene, 293, 191-198.
13. Doudna, J. A. (1995). Structure, 3, 747-750.
14. Ennifar, E. & Dumas, P. (2006). J. Mol. Biol. 356, 771-782.
15. Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C. & Dumas, P. (2001). Nature Struct. Biol. 8, 1064-1068.
16. François, B., Russell, R. J., Murray, J. B., Aboul-ela, F., Masquida, B., Vicens, Q. & Westhof, E. (2005). Nucleic Acids Res. 33, 5677-5690.
17. François, B., Szychowski, J., Adhikari, S. S., Pachamuthu, K., Swayze, E. E., Griffey, R. H., Migawa, M. T., Westhof, E. & Hanessian, S. (2004). Angew. Chem. Int. Ed. Engl. 43, 6735-6738.
18. Golden, B. L., Kim, H. & Chase, E. (2005). Nature Struct. Mol. Biol. 12, 82-89.
19. Han, Q., Zhao, Q., Fish, S., Simonsen, K. B., Vourloumis, D., Froelich, J. M., Wall, D. & Hermann, T. (2005). Angew. Chem. Int. Ed. Engl. 44, 2694-2700.
20. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F. & Yonath, A. (2001). Cell, 107, 679-688.
21. Ikawa, Y., Fukada, K., Watanabe, S., Shiraishi, H. & Inoue, T. (2002). Structure, 10, 527-534.
22. Inglehearn, C. F. & Cooke, H. J. (1990). Nucleic Acids Res. 18, 471-476.
23. International Human Genome Sequencing Consortium (2001). Nature (London), 409, 860-921.
24. International Human Genome Sequencing Consortium (2004). Nature (London), 431, 931-945.
25. Jaeger, L. & Chworos, A. (2006). Curr. Opin. Struct. Biol. 16, 531-543.
26. Jaeger, L. & Leontis, N. B. (2000). Angew. Chem. Int. Ed. Engl. 39, 2521-2524.
27. Jaeger, L., Westhof, E. & Leontis, N. B. (2001). Nucleic Acids Res. 29, 455-463.
28. Joshua-Tor, L., Frolow, F., Appella, E., Hope, H., Rabinovich, D. & Sussman, J. L. (1992). J. Mol. Biol. 225, 397-431.
29. Kasai, K., Nakamura, Y. & White, R. (1990). J. Forensic Sci. 35, 1196-1200.
30. Kondo, J., Adachi, W., Umeda, K., Sunami, T. & Takénaka, A. (2004). Nucleic Acids Res. 32, 2541-2549.
31. Kondo, J., François, B., Russell, R. J., Murray, J. B. & Westhof, E. (2006). Biochimie, 88, 1027-1031.
32. Kondo, J., François, B., Urzhumtsev, A. & Westhof, E. (2006). Angew. Chem. Int. Ed. Engl. 45, 3310-3314.
33. Kondo, J., Tanashaya, C., Juan, E. C. M., Sato, Y., Mitomi, K., Shimizu, S. & Takénaka, A. (2006). Nucleosides Nucleotides Nucleic Acids, 25, 693-704.
34. Kondo, J., Umeda, U., Fujita, K., Sunami, T. & Takénaka, A. (2004). J. Synchrotron Rad. 11, 117-120.
35. Kondo, J., Urzhumtsev, A. & Westhof, E. (2006). Nucleic Acids Res. 34, 676-685.
36. Leontis, N. & Westhof, E. (2001). RNA, 7, 499-512.
37. Leslie, A. G. W. (1992). Crystallography Computing 5. From Chemistry to Biology, edited by D. Moras, A. D. Podjarny & J. C. Thierry, pp. 50-61. Oxford University Press.
38. Liu, B., Baudrey, S., Jaegar, L. & Bazan, G. C. (2004). J. Am. Chem. Soc. 126, 4076-4077.
39. Lu, X. J. & Olson, W. K. (2003). Nucleic Acids Res. 31, 5108-5121.
40. McCouch, S. R., Teytelman, L., Xu, Y., Lobos, K. B., Clare, K., Walton, M., Fu, B., Maghirang, R., Li, Z., Xing, Y., Zhang, Q., Kono, I., Yano, M., Fjellstrom, R., DeClerck, G., Schneider, D., Cartinhour, S., Ware, D. & Stein, L. (2002). DNA Res. 9, 199-207.
41. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
42. Nasalean, L., Baudrey, S., Leontis, N. & Jaeger, L. (2006). Nucleic Acids Res. 34, 1381-1392.
43. Natrajan, G., Lamers, M. H., Enzlin, J. H., Winterwerp, H. H., Perrakis, A. & Sixma, T. K. (2003). Nucleic Acids Res. 31, 4814-4821.
44. Nunn, C. M. & Neidle, S. (1996). J. Mol. Biol. 256, 340-351.
45. Patel, D. J., Bouaziz, A., Kettani, A. & Wang, Y. (1999). Nucleic Acid Structure, edited by S. Neidle, pp. 389-453. Oxford University Press.
46. Pley, H. W., Flaherty, K. M. & McKay, D. B. (1994). Nature (London), 372, 68-74.
47. Powell, H. R. (1999). Acta Cryst. D55, 1690-1695.
48. Rossmann, M. G. & van Beek, C. G. (1999). Acta Cryst. D55, 1631-1640.
49. Sato, Y., Mitomi, K., Sunami, T., Kondo, J. & Takénaka, A. (2006). J. Biochem. 140, 759-762.
50. Sayle, R. A. & Milner-White, E. J. (1995). Trends Biochem. Sci. 20, 374.
51. Schuwirth, B. S., Borovinskaya, M. A., Hau, C. W., Zhang, W., Vila-Sanjurjo, A., Holton, J. M. & Cate, J. H. (2005). Science, 310, 827-834.
52. Scott, W. G., Finch, J. T. & Klug, A. (1995). Cell, 81, 991-1002.
53. Shandrick, S., Zhao, Q., Han, Q., Ayida, B. K., Takahashi, M., Winters, G. C., Simonsen, K. B., Vourloumis, D. & Hermann, T. (2004). Angew. Chem. Int. Ed. Engl. 43, 3177-3182.
54. Shibuya, H., Collins, B. K., Collier, L. L., Huang, T. H., Nonneman, D. & Johnson, G. S. (1996). Anim. Genet. 27, 59-60.
55. Stahley, M. R. & Strobel, S. A. (2005). Science, 309, 1587-1590.
56. Steller, I., Bolotovsky, R. & Rossmann, M. G. (1997). J. Appl. Cryst. 30, 1036-1040.
57. Su, L., Chen, L., Egli, M., Berger, J. M. & Rich, A. (1999). Nature Struct. Biol. 6, 285-292.
58. Sunami, T., Kondo, J., Hirao, I., Watanabe, K., Miura, K. & Takénaka, A. (2004a). Acta Cryst. D60, 90-96.
59. Sunami, T., Kondo, J., Hirao, I., Watanabe, K., Miura, K. & Takénaka, A. (2004b). Acta Cryst. D60, 422-431.
60. Sunami, T., Kondo, J., Kobuna, T., Hirao, I., Watanabe, K., Miura, K. & Takénaka, A. (2002). Nucleic Acids Res. 30, 5253-5260.
61. Takimoto-Kamimura, M., Takenaka, A. & Sasada, Y. (1986). Acta Cryst. C42, 601-603.
62. Terwilliger, T. C. & Berendzen, J. (1999). Acta Cryst. D55, 849-861.
63. Vicens, Q. & Westhof, E. (2001). Structure, 9, 647-658.
64. Vicens, Q. & Westhof, E. (2002). Chem. Biol. 9, 747-755.
65. Vicens, Q. & Westhof, E. (2003). J. Mol. Biol. 326, 1175-1188.
66. Westhof, E., Masquida, B. & Jaeger, L. (1996). Fold Des. 1, 78-88.
67. Williams, S., Hayes, L., Elsenboss, L., Williams, A., Andre, C., Abramson, R., Thompson, J. F. & Milos, P. M. (1997). Gene, 197, 101-107.
68. Wimberly, B. T., Brodersen, D. E., Clemons, W. M. Jr, Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T. & Ramakrishnan, V. (2000). Nature (London), 407, 327-339.
69. Xiong, Y. & Sundaralingam, M. (2000). RNA, 6, 1316-1324.
70. Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. & Noller, H. F. (2001). Science, 292, 883-896.
71. Zhang, L. & Doudna, J. A. (2002). Science, 295, 2084-2088.
72. Zhao, F., Zhao, Q., Blount, K. F., Han, Q., Tor, Y. & Hermann, T. (2005). Angew. Chem. Int. Ed. Engl. 44, 2-6.