Conformations of the sugar-phosphate backbone in helical DNA crystal structures

Biopolymers - Nucleic Acid Sciences Section

Volumn 42, Issue 1, 1997, Pages 113-124

  Schneider, Bohdan ^a   Neidle, Stephen ^a   Berman, Helen M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Crystal structures; DNA backbone; DNA conformations; Dna geometries; Structural databases

Indexed keywords

DNA BACKBONE GEOMETRY; OLIGODEOXY NUCLEOTIDES; TORSION ANGLES;

ANGLE MEASUREMENT; CONFORMATIONS; CRYSTAL STRUCTURE; PHOSPHATES; SUGARS;

DNA;

ARTICLE; CRYSTAL STRUCTURE; DATA BASE; DNA CONFORMATION; DNA SEQUENCE; MOLECULAR INTERACTION;

CRYSTALLOGRAPHY, X-RAY; DATABASES, NUCLEIC ACID; DNA; NUCLEIC ACID CONFORMATION; SUGAR PHOSPHATES;

EID: 0031195002     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(199707)42:1<113::aid-bip10>3.0.co;2-o     Document Type: Article

References (107)

1. Oison, W. K. (1982) in Topics in Nucleic Acid Structures, Part 2, S. Neidle, Ed., Macmillan Press, London, pp. 1 -79.
2. Pearlman, D. A. & Kim, S. H. ( 1988) Biopolymers 27, 59-77.
3. Sundaralingam, M. (1969) Biopolymers 7, 821-860.
4. Kim, S., Berman, H. M., Newton, M. D. & Seeman, N. C. (1973) Acta Crystallogr. B29, 703-710.
5. Yathindra, N. & Sundaralingam, S. M. ( 1973) Biopolymers 12, 297-314.
6. Sussman, J. L., Seeman, N. C., Kim, S. & Berman, H. M. (1972) J. Mol. Biol. 66, 403-421.
7. Rubin, J., Brennan, T. & Sundaralingam, M. ( 1972) Biochemistry 11,3112-3128.
8. Drew, H. R., Wing, R. M., Takano, T., Broka, C, Tanaka, S., Itakura, K. & Dickerson, R. E. (1981) Proc. Natl. Acad. Sei. USA 78, 2179-2183.
9. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. A. & Rieh, A. (1979) Nature 282, 680-686.
10. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992) Biophys. J. 63,751-759.
11. Ramachandran, G. N. & Sasisekharan, V. (1968) Adv. Protein Chem. 23, 283-437.
12. Westbrook, J., Demeny, T. & Hsieh, S.-H. (1992) NDBQuery-A Simplified User Interface to the Nucleic Acid Database, Rutgers University, New Brunswick, NJ.
13. Conner, B. N., Yoon, C., Dickerson, J. L. & Dickerson, R. E. (1984) J. Mol. Biol. 174, 663-695.
14. McCall, M., Brown, T. & Kennard, O. (1985) J. Mol. Biol. 183, 385-396.
15. Lauble, H., Frank, R., Blocker, H. & Heinemann, U. (1988) Nucleic Acids Res. 16, 7799-7816.
16. Heinemann, U., Lauble, H., Frank, R. & Bloecker, H. (1987) Nucleic Acids Res. 15, 9531-9550.
17. Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W. B. T., Salisbury, S. A. & Viswamitra, M. A. (1983) J. Mol. Biol. 166, 183-201.
18. Haran, T. E., Shakked, Z., Wang, A. H.-J. & Rich, A. (1987) J. Biomol. Struct. Dynam. 5, 199-217.
19. Jain, S. C., Zon, G. & Sundaralingam, M. (1989) Biochemistry 28, 2360-2364.
20. Hunter, W. N., D'Estaintot, B. L. & Kennard, O. (1989) Biochemistry' 28, 2444-2451.
21. Courseille, C., Dautant, A., Hospital, M., D'Estaintot, B. L., Precigoux, G., Molko, D. & Téoule, R. (1990) Acta Crystallogr. A46, FC9-FC12.
22. Takusagawa, F. (1990) J. Biomol. Struct. Dynam. 7, 795-809.
23. Shakked, Z., Guerstein-Guzikevich, G., Eisenstein, M., Frolow, F. & Rabinovich, D. (1989) Nature 342, 456-460.
24. Eisenstein, M., Hope, H., Haran, T. E., Frolow, F., Shakked, Z. & Rabinovich, D. (1988) Acta Crystallogr. B44, 625-628.
25. Eisenstein, M., Frolow, F., Shakked, Z. & Rabinovich, D. ( 1990) Nucleic Acids Res. 18,3185-3194.
26. Thota, N., Li, X. H., Bingman, C. & Sundaralingam, M. (1992) Acta Crystallogr. D49, 282-291.
27. Cervi, A., D'Estaintot, B. L. & Hunter, N. (1992) Acta Crystallogr. B48, 714-719.
28. Bingman, C., Li, X., Zon, G. & Sundaralingam, M. (1992) Biochemistry 31, 12803-12812.
29. Kamitori, S. & Takusagawa, F. (1994) J. Am. Chem. Soc. 116,4154-4165.
30. Kennard, O., Cruse, W. B. T., Nachman, J., Prange, T., Shakked, Z. & Rabinovich, D. ( 1986) J. Biomol. Struct. Dynam. 3, 623-647.
31. McCall, M., Brown, T., Hunter, W. N. & Kennard, O. (1986) Nature 322, 661-664.
32. Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., van der Marel, G. A., van Boom, J. H., Rieh, A. & Wang, A. H.-J. ( 1989) Eur. J. Biochem. 181, 295-307.
33. Ramakrishnan, B. & Sundaralingam, M. (1993) J. Mol. Biol. 231,431-444.
34. Ramakrishnan, B. & Sundaralingam, M. (1993) Biochemistry' 22, 11458-11468.
35. Verdaguer, N., Ayamani, J., Fernandez-Forner, D., Fita, L, Coll, M., Huynh-Dinh, T., Igolen, J. & Subirana, J. A. (1991) J. Mol. Biol 221, 623-635.
36. Bingman, C. A., Zon, G. & Sundaralingam, M. (1992) J. Mol. Biol. 227, 738-756.
37. Bingman, C., Jain, S., Zon, G. & Sundaralingam, M. ( 1992) Nucleic Acids Res. 20, 6637-6647.
38. Heinemann, U. & Alings, C. (1989) J. Mol. Biol. 210, 369-381.
39. Privé, G. G., Yanagi, K. & Dickerson, R. E. ( 1991 ) J.Mol. Biol. 217, 177-199.
40. Grzeskowiak, K., Yanagi, K., Privé, G. G. & Dickerson, R. E. ( 1991 ) J. Biol. Chem. 266,8861-8883.
41. Quintana, J. R., Grzeskowiak, K., Yanagi, K. & Dickerson, R.E. (1992) J. Mol. Biol. 225, 379-395.
42. Yuan, H., Quintana, J. & Dickerson, R. E. (1992) Biochemistry 31, 8009-9021.
43. Heinemann, U., Alings, C. & Bansal, M. (1992) EMBOJ. 11, 1931-1939.
44. Goodsell, D. S., Kopka, M. L., Cascio, D. & Dickerson, R. E. (1993) Proc. Natl. Acad. Sei. USA 90, 2930-2934.
45. Grzeskowiak, K., Goodsell, D. S., Kaczor-Grzeskowiak, M., Cascio, D. & Dickerson, R.E. (1993) Biochemistry 32, 8923-8931.
46. Goodsell, D. S., Kaczor-Grzeskowiak, M. & Dickerson, R. E. (1994) J. Mol. Biol. 239, 79-96.
47. Heinemann, U. & Hahn, M. ( 1992) J. Biol. Chem. 267, 7332-7341.
48. Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R.E. (1993) Biochemistry 32, 1373-1380.
49. Baikalov, I., Grzeskowiak, K., Yanagi, K., Quintana, J. & Dickerson, R.E. (1993) J. Mol. Biol. 231, 768-784.
50. Hahn, M. & Heinemann, U. (1993) Acta Crystallogr. D49, 468-477.
51. Drew, H. R., Samson, S. & Dickerson, R. E. ( 1982) Proc. Natl. Acad. Sei. USA 79, 4040-4044.
52. Holbrook, S. R., Dickerson, R.E. & Kim, S.-H. (1985) Acta Crystallogr. B41, 255-262.
53. Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987) Nature 330, 221-226.
54. Yoon, C., Prive, G. G., Goodsell, D. S. & Dick-erson, R. E. (1988) Proc. Natl. Acad. Sei. USA 85, 6332-6336.
55. DiGabriele, A. D., Sanderson, M. R. & Steitz, T. A. (1989) Proc. Natl. Acad. Sei. USA 86, 1816-1820.
56. Westhof, E. (1987) J. Biomol. Struct. Dynam. 5, 581-600.
57. Aymani, J., Coll, M., van der Marel, G. A., van Boom, J.H., Wang, A. H.-J. & Rieh, A. (1990) Proc. Natl. Acad. Sei. USA 87, 2526-2530.
58. Narayana, N., Ginell, S. L., Russu, I. M. & Herman, H. M. (1991) Biochemistry 30, 4449-4455.
59. Larsen, T. A., Kopka, M. L. & Dickerson, R. E. ( 1991 ) Biochemistry 30, 4443-4449.
60. Edwards, K. J., Brown, D. G., Spink, N. & Neidle, S. (1992) J. Mol. Biol. 226, 1161-1173.
61. Leonard, G. A. & Hunter, W. N. (1993) J. Mol. Biol. 234, 198-208.
62. DiGabriele, A.D. & Steitz, T. A. (1993) J. Mol. Biol. 231, 1024-1039.
63. Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. ( 1982) J. Biol. Chem. 257, 14686-14707.
64. Frederick, C. A., Quigley, G. J., van der Marel, G. A., van Boom, J. H., Wang, A. H.-J. & Rieh, A. (1988) J. Biol. Chem. 263, 17872-17879.
65. Xuan, J. C. & Weber, I. T. (1992) Nucleic Acids Res. 20, 5457-5464.
66. Cruse, W. B. T., Egert, E., Kennard, O., Sala, G. B., Salisbury, S. A. & Viswamitra, M. A. (1983) Biochemistry 22, 1833-1839.
67. Coll, M., Solans, X., Font-Altaba, M. & Subirana, J. A. (1987) J. Biomol. Struct. Dynam. 4,797-811.
68. Camerman, N., Fawcett, J. K. & Camerman, A. (1976) J. Mol. Biol. 107, 601-621.
69. Frederick, C. A., Coll, M., van der Marel, G. A., van Boom, J. H. & Wang, A. H.-J. ( 1988) Biochemistry 27,8350-3361.
70. Viswamitra, M. A., Shakked, Z., Jones, P. G., Sheldrick, G. M., Salisbury, S. A. & Kennard, O. (1982) Biopolymers 21, 513-533.
71. Kang, C. H., Berger, I., Lockshin, C., Ratliff, R., Moyzis, R. & Rich, A. (1995) Proc. Natl. Acad. Sei. USA 92, 3874-3878.
72. Leonard, G. A., Zhang, S., Peterson, M. R., Harrop, S. J., Helliwell, J. R., Cruse, W. B. T., D'Estaintot, B. L., Kennard, O., Brown, T. & Hunter, W. N. (1995) Structure 3, 335-340.
73. Kang, C., Zhang, X. H., Ratliff, R., Moyzis, R. & Rich, A. (1992) Nature 356, 126-131.
74. Joshua-Tor, L., Appella, E., Frolow, F., Hope, H., Rabinovich, D. & Sussman, J. L. (1992) J. Mol. Biol. 225, 397-431.
75. Chattopadhyaya, R., Grzeskowiak, K. & Dickerson, R.E. (1990) J. Mol. Biol. 211, 189-210.
76. Ramakrishnan, B. & Viswamitra, M. A. (1988) J. Biomol. Struct. Dynam. 6, 511-523.
77. Drew, H. R. & Dickerson, R.E. (1981) J. Mol. Biol. 152, 723-736.
78. Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A. & Wang, A. H.-J. (1989) J. Biol. Chem. 264,7921-7935.
79. Kagawa, T. F., Geierstanger, B. H., Wang, A. H.-J. & Ho, P. S. (1991) J. Biol. Chem. 266, 20175-20184.
80. Egli, M., Williams, L. D., Gao, Q. & Rich, A. (1991) Biochemistry 30, 11388-11402.
81. Bancroft, D., Williams, L. D., Rich, A. & Egli, M. (1994) Biochemistry 33, 1073-1086.
82. Doi, M., Inoue, M., Tomoo, K., Ishida, T., Ueda, Y., Akagi, M. & Urata, H. (1993) J. Am. Chem. Soc. 115, 10432-10433.
83. Fujii, S., Wang, A. H.-J., van der Marel, G., van Boom, J. H. & Rich, A. ( 1982) Nucleic Acids Res. 10, 7879-7892.
84. Chevrier, B., Dock, A. C., Hartmann, B., Leng, M., Moras, D., Thuong, M. T. & Westhof, E. J. ( 1986) J. Mol. Biol. 188, 707-719.
85. Wang, A. H.-J., Hakoshima, T., van der Marel, G. A., van Boom, J. H. & Rich, A. (1984) Cell 37, 321-331.
86. Geierstanger, B. H., Kagawa, T. F., Chen, S.-L., Quigley, G. J. & Ho, P.S. (1991) J. Biol. Chem. 266,20185-20191.
87. Coll, M., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H. & Rich, A. (1986) J. Biomol. Struct. Dynam. 4, 157-172.
88. Ginell, S. L., Kuzmich, S., Jones, R. A. & Berman, H. M. (1990) Biochemistry 29, 10461-10465.
89. Zhou, G. W. & Ho, P. S. (1990) Biochemistry 29, 7229-7236.
90. van Meerveit, L. V., Moore, M. H., Lin, P. K. T., Brown, D. M. & Kennard, O. (1990) J. Mol. Biol. 216, 773-781.
91. Schneider, B., Ginell, S. L., Jones, R., Gaffney, B. & Berman, H. M. (1992) Biochemistry 31, 9622-9628.
92. Cervi, A. R., Guy, A., Leonard, G. A., Teoule, R. & Hunter, W. N. ( 1993) Nucleic Acids Res. 21,5623-5629.
93. Schroth, G. P., Kagavva, T. F. & Ho, P. S. ( 1993) Biochemistry 32, 13381-13392.
94. Kumar, V. D., Harrison, R. W., Andrews, L. C. & Weber, I. T. (1992) Biochemistry 31, 1541-1550.
95. Brennan, R. G., Westhof, E. & Sundaralingam, M. (1986) J. Biomol. Struct. Dynam. 3, 649-665.
96. Broyde, S. B., Wartell, R. M., Stellman, S.D., Hingerty, B. & Langridge, R. (1975) Biopolymers 14, 1597-1613.
97. Viswamitra, M. A., Reddy, B. S., Lin, G. H.-Y. & Sundaralingam, M. (1971) J. Am. Chem. Soc. 93, 4565-4572.
98. Dickerson, R. E. & Drew, H. R. ( 1981 ) Proc. Natl. Acad. Sei. USA 78, 7318-7322.
99. Newton, M. D. ( 1973) J. Ain. Chem. Soc. 95, 256-258.
100. Lemieux, R. U. ( 1971 ) Pure Appl. Chem. 25, 527-548.
101. Cruse, W. B. T., Salisbury, S. A., Brown, T., Cosstick, R., Eckstein, F. & Kennard, O. ( 1986) J. Mol. Biol. 192, 891-905.
102. Privé, G. G., Heinemann, U., Chandrasegaran, S., Kan, L., Kopka, M. L. & Dickerson, R. E. (1987) Science 238, 498-504.
103. Gorenstein, D. G. (1994) Chem. Rev. 94, 1315-1338.
104. Chandrasekaran, R. & Amott, S. ( 1989) in LandoltBô'rnstein Numerical Data and Functional Relationships in Science and Technology, Group Vll/lb, Nucleic Acids, Saenger, W., Ed., Springer-Verlag, Berlin.
105. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., van der Marel, G. A., van Boom, J. H. & Rieh, A. ( 1981 ) Science 211, 171-176.
106. Brünger, A. T. ( 1992) X-PLOR, Version 3. 1. A System for X-Ray Crystallography and NMR, Yale University Press, New Haven, CT.
107. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. ( 1995) Acta Cry st. D 52, 57-64.