Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 Å Resolution and a 19 base pair duplex at 1.55 Resolution

Biochemistry

Volumn 38, Issue 45, 1999, Pages 14784-14792

  Klosterman, Peter S ^a   Shah, Sapan A ^a,b   Steitz, Thomas A ^a  

^a YALE UNIVERSITY   (United States)

^b MCKINSEY AND COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHATE; RNA; SUGAR; WATER;

ARTICLE; BASE PAIRING; CRYSTAL STRUCTURE; HYDRATION; MOLECULAR MODEL; NONHUMAN; PLASMID; PRIORITY JOURNAL; RNA SYNTHESIS;

CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PLASMIDS; RNA; WATER;

EID: 0033539650     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9912793     Document Type: Article

References (39)

1. Egli, M., Portmann, S., and Usman, N. (1996) Biochemistry 35, 8489-8494.
2. Correll, C. C., Freeborn, B., Moore, P. B., and Steitz, T. A. (1997) Cell 91, 705-712.
3. Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824.
4. Mueller, U., Schübel, H., Sprinzl, M., and Heinemann, U. (1999) RNA 5, 670-677.
5. Schneider, B., and Berman, H. M. (1995) Biophys. J. 69, 2661-2669.
6. Auffinger, P., and Westhof, E. (1998) J. Biomol. Struct. Dyn. 16, 693-707.
7. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R., and Schneider, B. (1992) Biophys. J. 63, 751-759.
8. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
9. Hagerman, P. J. (1997) Annu. Rev. Biophys. Biomol. Struct. 1997, 139-156.
10. Holbrook, S. R., Sussman, J. L., and Kim, S.-H. (1981) Science 212, 1275-1277.
11. Eguchi, Y., and Tomizawa, J. (1990) Cell 60, 199-209.
12. Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Nucleic Acids Res. 15, 8783-8798.
13. Predki, P. F., Nayak, L. M., Gottlieb, M. B., and Regan, L. (1995) Cell 80, 41-50.
14. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326.
15. CCP4 (1994) Acta Crystallogr. D50, 760-763.
16. Brünger, A. T. (1992) X-PLOR (Version 3.1): A System for X-ray Crystallography and NMR, Yale University, New Haven, CT.
17. Shah, S. A., and Brünger, A. T. (1999) J. Mol. Biol. 285, 1577-1588.
18. Terwilliger, T. C., and Berendzen, J. (1997) Acta Crystallogr. D53, 571-579.
19. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. A47, 110-119.
20. Brünger, A. T., Adams, P. D., DeLano, W., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Pannu, N. S., Read, R. J., Rice, L. M., and Simonson, T. (1998) Acta Crystallogr. D54, 905-921.
21. Sheldrick, G. M. (1997) SHELX-97, a Set of Programs for Crystal Structure Determination, University of Göttingen, Germany.
22. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T., and Berman, H. M. (1996) Acta Crystallogr. D52, 57-64.
23. Ondik, H., and Smith, D. (1962) in International Tables for X-ray Crystallography (Macgillavrly, C. H., and Rieck, G. D., Eds.) Vol. III, pp 257-274, Birmingham.
24. Wahl, M. C., Ban, C., Sekharudu, C., Ramakrishnan, B., and Sundralingam, M. (1996) Acta Crystallogr. D52, 655-667.
25. Pan, B., Mitra, S. N., and Sundralingam, M. (1999) Biochemistry 38, 2826-2381.
26. Tereshko, V., Gryaznov, S., and Egli, M. (1998) J. Am. Chem. Soc. 120, 269-283.
27. Zhang, H., van der Marel, G. A., van Boom, J. H., and Wang, A. H. (1992) Biopolymers 32, 1559-1569.
28. DiGabriele, A. D., and Steitz, T. A. (1993) J. Mol. Biol. 231, 1024-1039.
29. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G., and Rich, A. (1979) Nature 282, 680-686.
30. Drew, H., Takano, T., Tanaka, S., Itakura, K., and Dickerson, R. E. (1980) Nature 286, 567-573.
31. Egli, M., and Gessner, R. V. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 180-184.
32. Holbrook, S. R., and Kim, S. H. (1997) Biopolymers 44, 3-21.
33. Lavery, R., and Sklenar, H. (1988) J. Biomol. Struct. Dyn. 6, 63-91.
34. Chandrasekaran, R., and Arnott, S. (1989) in Landolt-Börnstein Numerical Data and Functional Relationships in Science and Technology, (Saenger, W., Ed.) Vol. VII/1b, pp 31-170, Springer-Verlag, Berlin.
35. de Leeuw, H. P. M., Haasnoot, C. A. G., and Altona, C. (1980) Isr. J. Chem. 20, 108-126.
36. Gelbin, A., Schneider, B., Clowney, L., Hsieh, S.-H., Olson, W. K., and Berman, H. M. (1996) J. Am. Chem. Soc. 118, 519-529.
37. Schneider, B., Cohen, D., and Berman, H. M. (1992) Biopolymers 32, 725-750.
38. Lommerse, J. P. M., Price, S. L., and Taylor, R. (1997) J. Comput. Chem. 18, 757-774.
39. Auffinger, P., and Westhof, E. (1997) J. Mol. Biol. 269, 326-341.