NMR and paramagnetic ion substitution locates a modified-nucleoside dependent metal binding site in DNA: Molecular dynamics, surface charge and H2O ordering

Magnetic Resonance in Chemistry

Volumn 34, Issue 13, 1996, Pages

  Agris, Paul F ^a   Stuart, John W ^a   Guenther, Richard ^a   Basti, Mufeed M ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NORTH CAROLINA A AND T STATE UNIVERSITY   (United States)

Author keywords

1H NMR; DNA solution conformation; Metal binding site; Modified nucleosides; NMR; Paramagnetic substitution; tRNA anticodon analogue

Indexed keywords

BIOMOLECULES; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARAMAGNETISM;

1H NMR; ANTICODONS; DNA SOLUTION CONFORMATION; DNA SOLUTIONS; METAL-BINDING SITES; MODIFIED NUCLEOSIDES; PARAMAGNETIC IONS; PARAMAGNETIC SUBSTITUTION; SOLUTION CONFORMATIONS; TRNA ANTICODON ANALOG;

DNA;

EID: 0030367615     PISSN: 07491581     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-458x(199612)34:133.0.co;2-y     Document Type: Article

References (44)

1. G. R. Bjork, in Transfer RNA in Protein Synthesis, edited by D. L. Hatfield, B. J. Lee and R. M. Pirtle, pp. 23-85. CRC Press, Boca Raton, FL (1992).
2. P. F. Agris, Prog. Nucl. Acids Res. Mol. Biol. 53, 79 (1996).
3. P. F. Agris, in Encyclopedia of NMR, edited by D. M. Grant and R. K. Harris, pp. 4151-4158. Wiley, Chichester (1996).
4. K. B. Hall, J. R. Sampson, O. C. Uhlenbeck and A. G. Redfield, Biochemistry 28, 5794 (1989).
5. C. S. Chow, L. S. Behlen, O. C. Uhlenbeck and J. K. Barton, Biochemistry 31, 972 (1992).
6. J. R. Sampson, L. S. Behlen, A. B. DiRenzo and O. C. Uhlenbeck, Biochemistry 31, 4161 (1992).
7. G. Striker, D. Labuda and M. C. Vega-Martin, J. Biomol. Struct. Dyn. 7, 235 (1989).
8. D. Yue, A. Kintanar and J. Horowitz, Biochemistry 33, 8905 (1994).
9. P. G. Schmidt, H. Sierzputowska-Gracz and P. F. Agris, Biochemistry 26, 8529 (1987).
10. P. G. Schmidt, T. Playl and P. F. Agris, Biochemistry 22, 1408 (1983).
11. P. F. Agris and P. G. Schmidt, Nucleic Acids Res. 8, 2085 (1980).
12. B. Honig and A. Nicholls, Science 268, 1144 (1995).
13. J. Swiatek, J. Coord. Chem. 33, 191 (1994).
14. S. H. Kim, F. L. Suddath, G. J. Quigley, A. McPherson, J. L. Sussman, A. H. J. Wang, N. C. Seeman and A. Rich, Science 185, 435 (1974).
15. G. J. Quigley, M. M. Teeter and A. Rich, Proc. Natl. Acad. Sci. USA 75, 64 (1978).
16. S. S. Reid and J. A. Cowan, Biochemistry 29, 6025 (1990).
17. V. Dao, R. Guenther, A. Malkiewicz, B. Nawrot, E. Sochacka, A. Kraszewski, K. Everett and P. F. Agris, Proc. Natl. Acad. Sci. USA, 91, 2125 (1994).
18. G. M. Clore, A. M. Gronenborn, E. A. Piper, L. W. McLaughlin, E. Graeser and J. H. van Boom, Biochem. J. 221, 737 (1984).
19. Y. Chen, H. Sierzputowska-Gracz, R. Guenther, K. Everett and P. F. Agris, Biochemistry 32, 10249 (1993).
20. R. H. Guenther, C. C. Hardin, H. Sierzputowska-Gracz and P. F. Agris, Biochemistry 31, 11004 (1992).
21. V. Dao, R. H. Guenther and P. F. Agris, Biochemistry 31, 11012 (1992).
22. M. M. Basti, J. Stuart, A. T. Lam, R. Guenther and P. F. Agris, Nature Struct. Biol. 3, 38 (1996).
23. N. D. Sincha, J. Biernat, J. McManus and H. Koster, Nucleic Acids Res. 12, 4539 (1984).
24. P. F. Agris, A. Malkiewicz, S. Brown, A. Kraszewski, B. Nawrot, E. Sochacka, K. Everett and R. Guenther, Biochimie 77, 125 (1995).
25. C. W. Gehrke, J. A. Desgres, K. O. Gerhardt, P. F. Agris, G. Keith, H. Sierzputowska-Gracz, M. S. Tempesta and K. C. Kuo, in Chromatography and Modification of Nucleosides, edited by C. W. Gehrke and K. C. Kuo, pp. 159-223. Elsevier, Amsterdam (1990).
26. C. R. Cantor, C. R. Warshaw and H. Shapiro, Biopolymers 9, 1059 (1970).
27. L. A. Marky and K. J. Breslauer, Biopolymers 26, 1601 (1987).
28. D. G. Davis and A. Bax, J. Am. Chem. Soc. 107, 2820 (1985).
29. G. Wagner and E. R. P. Zuiderweg, Biochem. Biophys. Res. Commun. 113, 854 (1983).
30. J. Williamson and S. G. Boxer, Biochemistry 28, 2819 (1989).
31. A. Kumar, R. R. Ernst and K. Wuthrich, Biochem. Biophys. Res. Commun. 95, 1 (1980).
32. D. J. States, R. A. Haberkorn and D. J. Ruben, J. Magn. Reson. 48, 286 (1982).
33. G. Drobny, A. Pines, A. Sinton, D. P. Weitkamp and D. E. Wemmer, Fararday Symp. Chem. Soc. 13, 49 (1979).
34. S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case, J. Comput. Chem. 7, 230 (1986).
35. A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991).
36. K. Wüthrich, NMR of Proteins and Nucleic Acids. Wiley, New York (1988).
37. J. Lingbeck, M. G. Kubinec, J. Miller, B. R. Reid, G. P. Drobny and M. A. Kennedy, Biochemistry 35, 719 (1996).
38. C. A. G. Haasnoot, H. P. Westerink, G. A. van der Marel and J. H. van Boom, J. Biomol. Struct. Dyn. 2, 345 (1984).
39. W. Bujalowski, E. Greser, L. W. McLaughlin and D. Porschke, Biochemistry 25, 6365 (1986).
40. A. T. Lam, R. Guenther and P. F. Agris, BioMetals 8, 290 (1995).
41. G. Ott, L. Arnold and S. Limmer, Nucleic Acids Res. 21, 5859 (1993).
42. K. A. Sharp, B. Honig and S. C. Harvey, Biochemistry 29, 340 (1990).
43. E. Draper, Acc. Chem. Res. 25, 201 (1992).
44. P. F. Agris and S. C. Brown, Methods Enzymol. 261, 277 (1995).