FRET study of a trifluorophore-labeled DNAzyme

Journal of the American Chemical Society

Volumn 124, Issue 51, 2002, Pages 15208-15216

  Liu, Juewen ^a   Lu, Yi ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRIFLUOROPHORE;

BIOTECHNOLOGY; COMPLEXATION; DNA; DRUG PRODUCTS; ENERGY TRANSFER; FLUORESCENCE; MOLECULAR STRUCTURE; PROTEINS; RESONANCE;

MOLECULAR BIOLOGY;

DNA; ENZYME; FLUORINE DERIVATIVE; METAL ION; RIBOZYME; ZINC ION;

ARTICLE; BIOMOLECULAR ELECTRONICS; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; ENZYME ANALYSIS; FLUORESCENCE; MOLECULAR DYNAMICS; PROTEIN FOLDING; TECHNIQUE;

DNA, CATALYTIC; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; REPRODUCIBILITY OF RESULTS;

EID: 0037176245     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja027647z     Document Type: Article

References (47)

1. Clegg, R. M. Methods Enzymol. 1992, 211, 353-388.
2. Lorenz, M.; Hillisch, A.; Diekmann, S. Rev. Mol. Biotechnol. 2002, 82, 197-209.
3. Lilley. D. M. J.; Wilson, T. J. Curr. Opin. Chem. Biol. 2000, 4, 507-517.
4. Walter, N. G. Methods (Orlando, Fla) 2001, 25, 19-30.
5. Stuhmeier, F.; Welch, J. B.; Murchie, A. I. H.; Lilley, D. M. J.; Clegg, R. M. Biochemistry 1997, 36, 13530-13538.
6. Clegg, R. M.; Murchie, A. I. H.; Lilley, D. M. J. Biophys. J. 1994, 66, 99-109.
7. Gohlke, C.; Murchie, A. I. H.; Lilley, D. M. J.; Clegg, R. M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 11660-11664.
8. Bassi, G. S.; Murchie, A. I. H.; Walter, F.; Clegg, R. M.; Lilley, D. M. J. EMBO J. 1997, 16, 7481-7489.
9. Murray, J. B.; Seyhan, A. A.; Walter, N. G.; Burke, J. M.; Scott, W. G. Chem. Biol. 1998, 5, 587-595.
10. Walter, N. G.; Burke, J. M.; Millar, D. P. Nat. Struct. Biol. 1999, 6, 544-549.
11. Hampel, K. J.; Burke, J. M. Biochemistry. 2001, 40, 3723-3729.
12. Wilson, T. J.; Zhao. Z.-Y.; Maxwell, K.; Kontogiannis, L.; Lilley, D. M. J. Biochemistry 2001, 40, 2291-2302.
13. Pereira, M. J. B.; Harris, D. A.; Rueda, D.; Walter, N. G. Biochemistry 2002, 41, 730-740.
14. Jenne, A.; Gmelin, W.; Raffler, N.; Famulok, M. Angew. Chem., Int. Ed. 1999, 38, 1300-1303.
15. Fang, X.-W.; Pan. T.; Sosnick, T. R. Nat. Struct. Biol. 1999, 6, 1091-1095.
16. Wallace, M. I.; Ying, L.; Balasubramanian, S.; Klenerman, D. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5584-5589.
17. Parkhurst, K. M.; Brenowitz, M.; Parkhurst, L. J. Biochemistry 1996, 35, 7459-7465.
18. Didenko. V. V. BioTechniques 2001, 31, 1106-1121.
19. Taylor, D. L.; Reidler, J.; Spudich, J. A.; Stryer, L. J. Cell Biol. 1981, 89, 362-367.
20. Sawyer, W. H.; Chan, R. Y. S.; Eccleston, J. F.; Davidson, B. E.; Samat. S. A.; Yan, Y. Biochemistry, 2000, 39, 5653-5661.
21. Bhattacharyya, A.; Bhattacharyya, B.; Roy, S. Eur. J. Biochem. 1993, 216, 757-761.
22. Runnels, L. W.; Scarlata, S. F. Biophys. J. 1995, 69, 1569-1583.
23. Tong, A. K.; Jockusch, S.; Li, Z.; Zhu, H.-R.; Akins, D. L.; Turro, N. J.; Ju, J. J. Am. Chem. Soc. 2001, 123, 12923-12924.
24. Breaker, R. R.; Joyce, G. F. Chem. Biol. 1994, 1, 223-229.
25. Breaker, R. R. Nat. Biotechnol. 1997, 15, 427-431.
26. Sen, D.; Geyer, C. R. Curr. Opin. Chem. Biol. 1998, 2, 680-687.
27. Breaker, R. R. Nat. Biotechnol. 1999, 17, 422-423.
28. Lu, Y. Chem. Eur. J. 2002, 8, 4588-4596.
29. Santoro, S. W.; Joyce, G. F. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 4262-4266.
30. Li, J.; Lu, Y. J. Am. Chem. Soc. 2000, 122, 10466-10467.
31. Fahlman, R. P.; Sen, D. J. Am. Chem. Soc. 2002, 124, 4610-4616.
32. Stojanovic, M. N.; Mitchell, T. E.; Stefanovic, D. J. Am. Chem. Soc. 2002, 124, 3555-3561.
33. Faulhammer, D.; Famulok, M. Angew. Chem., Int. Ed. Engl. 1996, 35, 2837-2841.
34. Li, J.; Zheng, W.; Kwon, A. H.; Lu, Y. Nucleic Acids Res. 2000, 28, 481-488.
35. Peracchi, A. J. Biol. Chem. 2000, 275, 11693-11697.
36. Tuschl, T.; Gohlke, C.; Jovin, T. M.; Westhof, E.; Eckstein, F. Science 1994, 266, 785-789.
37. Lakowicz, J. R. Principles of Flourescence Spectroscopy; Plenum Press: New York, 1983.
38. Nickel, B. J. Lumin. 1989, 44, 1-18.
39. Förster, T. Ann. Physik 1948, 2, 55-75.
40. Fairclough, R. H.; Cantor, C. R. Methods Enzymol. 1978, 48, 347-379.
41. van der Meer, B. W. Rev. Mol. Biotechnol. 2002, 82, 181-196.
42. Grunwell, J. R.; Glass, J. L.; Lacoste, T. D.; Deniz, A. A.; Chemla, D. S.; Schultz, P. G. J. Am. Chem. Soc. 2001, 123, 4295-4303.
43. Bassi, G. S.; Mollegaard, N. E.; Murchie, A. I. H.; Lilley, D. M. J. Biochemistry 1999, 38, 3345-3354.
44. Li, J. Ph.D. Dissertation. University of Illinois at Urbana-Champaign, Urbana, IL, 2000.
45. Murray, J. B.; Terwey, D. P.; Maloney, L.; Karpeisky, A.; Usman, N.; Beigelman, L.; Scott, W. G. Cell 1998, 92, 665-673.
46. Peracchi, A.; Karpeisky, A.; Maloney, L.; Beigelman, L.; Herschlag, D. Biochemistry 1998, 37, 14765-14775.
47. Stage-Zimmermann, T. K.; Uhlenbeck, O. C. RNA 1998, 4, 875-889.