Non-Watson-Crick base associations in DNA and RNA revealed by single crystal x-Ray diffraction methods: Mismatches, modified bases, and nonduplex DNA

Biopolymers

Volumn 44, Issue 1, 1997, Pages 91-103

  Brown, Tom ^a   Hunter, William N ^b  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

DNA; G tetnid; Hydrogen bonds; Loop; Mismatches; Mispairs; Modified bases; Mutagenesis; Non Watson Crick base pairs; Quadruplexes; RNA; Triplexes; Watson Crick base pairs

Indexed keywords

CARCINOGENS; CHEMICAL MODIFICATION; CRYSTAL STRUCTURE; ENZYMES; HYDROGEN BONDS; MOLECULAR STRUCTURE; MUTAGENESIS; RNA; SINGLE CRYSTALS; X RAY CRYSTALLOGRAPHY;

NON WATSON CRICK BASE ASSOCIATIONS; SINGLE CRYSTAL X RAY DIFFRACTION METHODS;

DNA;

DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; OLIGONUCLEOTIDE; PURINE; PYRIMIDINE; RNA;

ARTICLE; BASE MISPAIRING; BASE PAIRING; CRYSTAL STRUCTURE; DNA DAMAGE; DNA HELIX; DNA STRUCTURE; HYDRATION; HYDROGEN BOND; RNA STRUCTURE; X RAY DIFFRACTION;

EID: 0031423669     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(1997)44:1<91::AID-BIP6>3.0.CO;2-V     Document Type: Article

References (66)

1. Watson, J. D. & Crick, F. H. C. (1953) Nature 171, 737-738.
2. Saenger, W. (1984) The Principles of Nucleic Acid Structure, Springer-Verlag, New York.
3. Loft, S. & Poulsen, H. E. (1996) J. Mol. Med. 74, 297-312.
4. Modrich, P. (1987) Ann. Rev. Biochem. 56, 435-466.
5. Pearl, L. H. & Savva, R. (1995) TIBS 20, 421-426.
6. Brown, T., Hunter, W. N. & Leonard, G. A. (1993) Chem. Brit. 6, 484-488.
7. Watson, J. D. & Crick, F. H. C. (1953) Nature 171, 964-966.
8. Topal, M. D. & Fresco, J. R. (1976) Nature 263, 290-293.
9. Strazewski, P. & Tamm, C. (1990) Angew. Chem. Intl. Edt. Engl. 29, 36-57.
10. Wing, R., Drew R. H., Takano, T., Broka, C., Takana, S., Itakura, K. & Dickerson, R.E. (1980) Nature 287, 755-758,
11. Kennard, O. & Hunter, W. N. (1991) Angew. Chemie 30, 1254-1277.
12. Brown, T., Kennard, O., Kneale, G. & Rabinovich, D. (1985) Nature 315, 604-606.
13. Hunter, W. N., Kneale, G., Brown, T., Rabinovich, D. & Kennard, O. (1986) J. Mol. Biol. 190, 605-618.
14. Kneale, G., Brown, T., Kennard, O. & Rabinovich, D. (1985) J. Mol. Biol. 186, 805-814.
15. Hunter, W. N., Brown, T., Kneale, G., Anand, N. N., Rabinovich, D. & Kennard, O. (1987) J. Biol. Chem. 262, 9962-9970.
16. Ho, P. S., Frederick, C. A., Quigley, G., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J. & Rich, A. (1985) EMBO J. 4, 3617-3623.
17. Crick, F. H. C. (1966) J. Mol Biol. 19, 548-555.
18. Brown, T., Kneale, G., Hunter, W. N. & Kennard, O. (1986) Nucleic Acids Res. 14, 1801-1809.
19. Coll, M., Saal, D., Frederick, C. A., Aymami, J., Rich, A. & Wang, A.-H. J. (1989) Nucleic Acids. Res. 17, 911-923.
20. Betzel, C., Lorenz, S., Furste, J. P., Bald, R., Zhang, M., Schneider, T., Wilson, K. S. & Erdmann, V. A. (1994) FEBS Lett. 351, 159-164.
21. Cruse, W. B. T., Aymami, J., Kennard, O., Brown, T., Jack, A. G. C. & Leonard, G. A. (1989) Nucleic Acids Res, 17, 55-72.
22. Hunter, W. N., Brown, T., Anand, N. N. & Kennard, O. (1986) Nature 320, 552-555.
23. Hunter, W. N., Brown, T. & Kennard, O. (1987) Nucleic Acids Res. 15, 6589-6606.
24. Brown, T., Leonard, G. A., Booth, E. D. & Kneale, G. (1990) J. Mol. Biol. 221, 437.
25. Fersht, A. R., Knill-Jones, J. W. & Tsui, W. C. (1982) J. Mol. Biol. 156, 37-51.
26. Prive, G. G., Heinemann, U., Kan, L. S., Chandrasegaran, S. & Dickerson, R. E. (1987) Science 238, 498-504.
27. Brown, T., Hunter, W. N., Kneale, G. G. & Kennard, O. (1986) Proc. Natl. Acad. Sci. USA 83, 2402-2406.
28. Brown, T., Leonard, G. A., Booth, E. D. & Chambers, J. (1989) J. Mol. Biol. 207, 455-457.
29. W. N. Hunter, Brown, T. & Kennard, O. (1986) J. Biomol. Struct. Dynam. 4, 173-191.
30. Leonard, G. A., McAuley-Hecht, K., Abel, S., Lough, D. M., Brown, T. & Hunter, W. N. (1994) Structure 2, 483-494.
31. Corfield, P. W. R., Hunter, W. N., Brown, T., Robinson, P. & Kennard, O. (1987) Nucleic Acids Res. 15, 7935-7949.
32. Webster. G. D., Sanderson, M. R., Skelly, J. V., Neidle, S., Swann, P. F., Li, B. F. & Tickle, I. (1990) Proc. Natl. Acad. Sci. USA 87, 6693-6697.
33. Leonard, G., Booth, E., Hunter, W. N. & Brown, T. (1992) Nucleic Acids Res. 20, 4753-4759.
34. Skelly, J. V., Edwards, K. J., Jenkins,T. C. & Neidle, S. (1993) Proc. Natl. Acad. Sci. USA 90, 804-808.
35. Holbrook, S. R., Cheong, C., Tinoco, I., Jr. & Kim, S. H. (1991) Nature 353, 579-581.
36. Baeyens, K. J., De Bondf, H. L. & Holbrook, S. R. (1995) Nature Struct. Biol 2, 56-62.
37. Lietzke, S. E., Barne, C. L., Bergland, J. A. & Kundrot, C. E. (1996) Structure 4, 917-930.
38. Cruse, W. B. T., Saludjian, P., Biala, E., Strazewski, P., Prange, T. & Kennard, O. (1994) Proc. Natl. Acad. Sci. 91, 4160-4164.
39. Wahl, M. C., Rao, S. T. & Sundaralingham, M. (1996) Nature Struct. Biol. 3, 24-30.
40. Leonard, G. A., McAuley-Hecht, K., Brown, T. & Hunter, W. N. (1995) Acta Cryst. D51, 136-139.
41. Leonard, G. A., Thomson, J. B., Watson, W. P. & Brown, T. (1990) Proc. Natl. Acad. Sci. USA 87, 9573-9576.
42. Ginell, S. L., Vojtechovsky, J., Gaffney, B., Jones, R. & Berman, H. M. (1994) Biochemistry 33, 3487-3493.
43. Vojtechovsky, J., Eaton, M. D., Gaffney, B., Jones, R. & Berman, H. M. (1994) Biochemistry 34, 16632-16640.
44. Leonard, G. A., McAuley-Hecht, K. E., Gibson, N. J., Brown, T., Watson, W. P. & Hunter, W. N. (1994) Biochemistry 33, 4755-4761.
45. Leonard, G. A., Guy, A., Brown, T., Teoule, R. & Hunter, W. N. (1992) Biochemistry 31, 8415-8420.
46. McAuley-Hecht, K. E., Leonard, G. A., Gibson, N.J., Thomson, J. B., Watson, W. P., Hunter, W. N. & Brown, T. (1994) Biochemistry 33, 1026610270.
47. Scoff, W. G. & Klug, A. (1996) TIBS 21, 220-224.
48. Gate, 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.
49. Van Meervelt, L., Dautant, A., Gallois, B., Precigoux, G. & Kennard, O. (1995) Nature 374, 742-744
50. Vlieghe, D., van Meervelt, L., Dautant, A., Gallois, B., Precigoux, G. & Kennard, O. (1996) Science 273, 1702-1705.
51. Betts, L., Josey, J. A., Veal, J. M. & Jordan, S. R. (1995) Science 270, 1838-1841.
52. Sen, D. & Gilbert, W. (1988) Nature 334, 364-366.
53. Sunquist, W. I. Klug, A. (1989) Nature 342, 825-829.
54. Williamson, J. R., Raghuraman, M. K. & Cech, T. R. (1989) Cell 59, 871-880.
55. Smith, F. W. & Feigon, J. (1992) Nature 356, 164-168.
56. Kang, C., Zhang, X., Ratcliff, R., Moyzis, R. & Rich, A. (1992) Nature 356, 126-131.
57. Laughlin, G., Murchie, A. I. H., Norman, D. G., Moore, M. H., Moody, P. C. E., Liliey, D. M. J. & Luisi, B. (1994) Science 265, 520-524.
58. Padmanabhan, K. & Tulinsky, A. (1996) Acte Cryst. D52, 272-282.
59. Chen, L., Cai, L., Zhang, X. & Rich, A. (1994) Biochemistry 33, 13540-3546.
60. Kang, C., Berger, I., Lockshin, C., Ratcliff, R., Moyzis, R. & Rich, A. (1994) Proc. Natl. Acad. Sci. USA 91, 11636-11640.
61. Berger, I., Kang, C., Fredian, A., Ratcliff, R., Moyzis, R. & Rich, A. (1995) Nature Struct. Biol. 2, 416-425.
62. Kang, C., Berger, I., Lockshin, C., Ratcliff, R., Moyzis, R. & Rich, A. (1995) Proc. Natl. Acad. Scl. USA 92, 3874-3878.
63. Leonard, G. A., Zhang, S., Peterson, M. R., Harrop, S. J., Helliwell, R., Cruse, W. B. T., Langlois d'Estaintot, B., Kennard, O., Brown, T. & Hunter, W. N. (1995) Structure 3, 335-340.
64. Chattopadhyaya, R., Ikuta, S., Grzeskowiak, K. & Dickerson, R. E. (1988) Nature 334, 175-179.
65. Chattopadhyaya, R., Grzeskowiak, K. & Dickerson, R. E. (1990) J. Mol. Biol 211, 189-210.
66. Kraulis, P. J. (1991) J. Appl. Crystallogr, 24, 946-950.