Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using raman crystallography

Journal of the American Chemical Society

Volumn 130, Issue 30, 2008, Pages 9670-9672

  Gong, Bo ^a   Chen, Yuanyuan ^a   Christian, Eric L ^a   Chen, Jui Hui ^b   Chase, Elaine ^b   Chadalavada, Durga M ^c   Yajima, Rieko ^c   Golden, Barbara L ^b   Bevilacqua, Philip C ^c   Carey, Paul R ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM HYDROXIDE; PHOSPHATE; RIBOZYME; VIRUS RNA;

ARTICLE; CALCULATION; CRYSTALLOGRAPHY; HEPATITIS DELTA VIRUS; MOLECULAR INTERACTION; MOLECULAR MODEL; RAMAN SPECTROMETRY; RNA BINDING; RNA STRUCTURE; SUBSTITUTION REACTION; VIRUS MORPHOLOGY;

CRYSTALLOGRAPHY, X-RAY; HEPATITIS DELTA VIRUS; MAGNESIUM HYDROXIDE; MODELS, MOLECULAR; PHOSPHORIC ACID ESTERS; RNA, CATALYTIC; SPECTRUM ANALYSIS, RAMAN;

EID: 48249121539     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja801861s     Document Type: Article

References (25)

1. Feig, A. L.; Uhlenbeck, O. C. The Role of Metal Ions in RNA Biochemistry. In The RNA World, 2nd ed.; Cold Spring Harbor Laboratory Press: Plainview, NY1999; p 287.
2. (a) DeRose, V. J. Curr. Opin. Struct. Biol. 2003, 13, 317.
3. (b) Sigel, R. K.; Pyle, A. M. Chem. Rev. 2007, 107, 97.
4. (a) Kieft, J. S.; Tinoco, I., Jr Structure 1997, 5, 317.
5. (b) Maderia, M.; Horton, T. E.; DeRose, V. J. Biochemistry 2000, 39, 8193.
6. (a) Hougland, J. L.; Kravchuk, A. V.; Herschlag, D.; Piccirilli, J. A. PloS Biol. 2005, 3, 1536.
7. (b) Maderia, M.; Hunsicker, L. M.; DeRose, V. J. Biochemistry 2000, 39, 12113.
8. Gong, B.; Chen, J. H.; Chase, E.; Chadalavada, D. M.; Yajima, R.; Golden, B. L.; Bevilacqua, P. C.; Carey, P. R. J. Am. Chem. Soc. 2007, 129, 13335.
9. Ferre-D'Amare, A. R.; Zhou, K.; Doudna, J. A. Nature 1998, 395, 567.
10. (a) Perrotta, A. T.; Shih, I.; Been, M. D. Science 1999, 286, 123.
11. (b) Nakano, S.; Chadalavada, D. M.; Bevilacqua, P. C. Science 2000, 287, 1493.
12. (c) Ke, A.; Zhou, K.; Ding, F.; Cate, J. H.; Doudna, J. A. Nature 2004, 429, 201.
13. (d) Das, S. R.; Piccirilli, J. A. Nat. Chem. Biol. 2005, 1, 45.
14. (e) Nakano, S.; Bevilacqua, P. C. Biochemistry 2007, 46, 3001.
15. Lai, M. M. Annu. Rev. Biochem. 1995, 64, 259.
16. 3 substitution at the U-1 position of the inhibitor strand and are surrounded by cacodylate buffer at pH 6.0.
17. Pye, C. C.; Rudolph, W. W. J. Phys. Chem. A 1998, 102, 9933.
18. 2+" conditions are achieved by soaking crystals in 50 mM EDTA, ∼5 times during 20 h.
19. (a) Carey, P. R. Biochemical Applications of Raman and Resonance Raman Spectroscopies; Academic Press: New York, 1982; Chapter 5.
20. (b) Guan, Y.; Wurrey, C. J.; Thomas, G. J., Jr Biophys. J. 1994, 66, 225.
21. Anderson, V. E.; Christian, E. L.; Harris, M. E. Private communication.
22. Peleg, M. J. Phys. Chem 1972, 76, 1019.
23. Juneau, K.; Podell, E.; Harrington, D.; Cech, T. R. Structure 2001, 9, 221.
24. Nakano, S.; Proctor, D. J.; Bevilacqua, P. C. Biochemistry 2001, 40, 12022.
25. Carey, P. R. Chem. Rev. 2006, 106, 3034.