Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy

Chemistry and Biology

Volumn 6, Issue 11, 1999, Pages 801-810

  Feig, Andrew L ^a,c   Panek, Mark ^b   Horrocks Jr , William DeW ^b   Uhlenbeck, Olke C ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

Europium; Lanthanide; Metal binding; RNA; Terbium

Indexed keywords

EID: 0033231004     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(99)80127-6     Document Type: Article

References (56)

1. McKay, D.B. & Wedekind, J.E. (1998). Small ribozymes. In The RNA World. (Gesteland, R., Cech, T., & Atkins, J., eds) pp. 265-286, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
2. McKay, D.B. (1996). Structure and function of the hammerhead ribozyme: An unfinished story. RNA 2, 395-403.
3. Hertel, K.J., Herschlag, D. & Uhlenbeck, O.C. (1994). A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33, 3374-3385.
4. Heidenreich, O. & Eckstein, F. (1997). Synthetic ribozymes: The hammerhead ribozyme. In Concepts in Gene Therapy. (Strauss, M. & Barranger, J., eds.) pp. 169-195, Walie de Gruyter, Berlin.
5. Thomson, J.B., Tuschl, T. & Eckstein, F. (1996). The hammerhead ribozyme. In Catalytic RNA. (Lilley, D.M.J. & Eckstein, F., eds) pp. 1 73-196, Springer-Verlag, Berlin.
6. Murray, J.B., et al., & Scott, W.G. (1998). The structural basis of hammerhead ribozyme self-cleavage. Cell 92, 665-673.
7. Scott, W.G., Finch, J.T. & Klug, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage. Cell 81, 991-1002.
8. Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. & Klug, A. (1996). Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme. Science 274, 2065-2069.
9. Pley, H.W., Flaherty, K.M. & McKay, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
10. Dahm, S.C. & Uhlenbeck, O.C. (1991 ). Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30, 9464-9469.
11. Feig, A.L. & Uhlenbeck, O.C. (1998). The role of metal ions in RNA biochemistry. In The RNA World. (Gesteland, R., Cech, T., & Atkins, J., eds) pp. 287-319, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
12. Long, D.M., LaRiviere, F.J. & Uhlenbeck, O.C. (1995). Divalent metal ions and the internal equilibrium of the hammerhead ribozyme. Biochemistry 34, 14435-14440.
13. Pan, T., Long, D.M. & Uhlenbeck, O.C. (1993). Divalent metal ions in RNA folding and catalysis. In The RNA World. (Gesteland, R. & Atkins, J., eds) pp. 271-302, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
14. Pyle, A.M. (1993). Ribozymes: A distinct class of metalloenzymes. Science 261, 709-714.
15. Pyle, A.M. (1996). Role of metal ions in ribozymes. In Interactions of Metal Ions with Nucleotides, Nucleic Acids, and their Constituents, Metal Ions in Biological Systems Vol. 32. (Sigel, A. & Sigel, H., eds.) pp. 479-520, Marcel Dekker, New York.
16. Peracchi, A., Beigelman, L., Scott, E.C., Uhlenbeck, O.C. & Herschlag, D. (1997). Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J. Biol. Chem. 272, 26822-26826.
17. Ruffner, D.E. & Uhlenbeck, O.C. (1990). Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction. Nucleic Acids Res. 18, 6025-6029.
18. Knöll, R., Bald, R. & Fürste, J.P. (1997). Complete identification of non-bridging phosphate oxygens involved in hammerhead cleavage. RNA 3, 132-140.
19. Scott, E.C. & Uhlenbeck, O.C. (1999). A re-investigation of the thio effect at the hammerhead cleavage site. Nucleic Acids Res. 27, 479-484.
20. Feig, A.L. Scott, W.G., & Uhlenbeck, O.C. (1998). Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb(III). Science 279, 81-84.
21. Ruffner, D.E., Stormo, G.D. & Uhlenbeck, O.C. (1990). Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695-10702.
22. Tuschl, T., Ng., M.M.P., Pieken, W., Benseler, F. & Eckstein, F. (1993). Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity. Biochemistry 32, 11658-11668.
23. Fu, D.-J., Rajur, S.B. & McLaughlin, L.W. (1993). Importance of specific guanosine N7-nitrogens and purine amino groups for efficient cleavage by a hammerhead ribozyme. Biochemistry 32, 10629-10637.
24. Slim, G. & Gait, M.J. (1992). The role of the exocyclic amino groups of conserved purines in hammerhead ribozyme cleavage. Biochem. Biophys. Res. Commun. 183, 605-609.
25. Bassi, G.S., Møllegaard, N.-E., Murchie, A.I.H., von Kitzing, E. & Lilley, D.M.J. (1995). Ionic interactions and the global conformations of the hammerhead ribozyme. Nat. Struct. Biol. 2, 45-55.
26. Bassi, G.S., Murchie, A.I.H. & Lilley, D.M.J. (1996). The ion-induced folding of the hammerhead ribozyme: Core sequence changes that perturb folding into the active conformation. RNA 2, 756-768.
27. Bassi, G.S., Murchie, A.I.H., Walter, F., Clegg, R.M. & Lilley, D.M J. (1997). Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study. EMBO J. 16, 7481-7489.
28. Horrocks, W.D., Jr. (1993). Luminescence spectroscopy. Methods Enzymol. 226, 495-538.
29. Horrocks, W.D., Jr. & Albin, M. (1991 ). Lanthanide ion luminescence in coordination chemistry and biochemistry. Prog. Inorg. Chem. 31, 1-104.
30. Horrocks, W.D., Jr. & Sudnick, D.R. (1979). Lanthanide ion probes of structure in biology, laser-induced luminescence decay constants provide a direct measure of the number of metal-coordinated water molecules. J. Am. Chem. Soc. 101, 334-340.
31. McNemar, C.W. & Horrocks, W.D., Jr. (1989). The resolution of laser-induced Eu(III) ion excitation spectra through the use of the Marquardt nonlinear regression method. Appl. Spectrosc. 43, 816-821.
32. Klakamp, S.L. & Horrocks, W.D., Jr. (1992). Lanthanide ion luminescence as a probe of DNA structure. 1. Guanine-containing oligomers and nucleotides. J. Inorg. Biochem. 46, 175-192.
33. Klakamp, S.L. & Horrocks, W.D., Jr. (1992). Lanthanide ion luminescence as a probe of DNA structure. 2. Non-guanine-containing oligomers and nucleotides. J. Inorg. Biochem. 46, 193-205.
34. 0 transition in Eu(III) complexes with the sum of nephelauxetic parameters for all of the coordinating atoms. Inorg. Chim. Acta 229, 383-390.
35. Kazakov, S.A. (1996). Nucleic acid binding and catalysis by metal ions. In Bioorganic Chemistry: Nucleic Acids. (Hecht, S.M., ed.) pp. 244-477, Oxford University Press, New York.
36. Huheey, J.E. (1983). Inorganic Chemistry. (Third Edition Edn.), Harper & Row, New York.
37. Draper, D.E. & Misra, V.K. (1998). RNA shows its metal. Nat. Struct. Biol. 5, 927-930.
38. Ma, J.-F., Jin, Z.-S. & Ni, J.-Z. (1994). Terbium p-nitrobenzoate hydrate. Acta Crystallogr. C 50, 1008-1010.
39. Kayne, M.S. & Cohn, M. (1974). Enhancement of Tb(III) and Eu(III) fluorescence in complexes with E. coli tRNA. Biochemistry 13, 4159-4165.
40. Wolfson, J.M. & Kearns, D.R. (1974). Europium as a fluorescent probe of metal binding sites on tRNA. I. Binding to E. coli formylmethionine tRNA. J. Am. Chem. Soc. 96, 3653-3654.
41. Draper, D.E. (1985). On the coordination properties of Eu(III) bound to tRNA. Biophys. Chem. 21, 91-101.
42. Phe. Ph.D. Thesis, Pennsylvania State University.
43. Jack, A., Ladner, J.E., Rhodes, D., Brown, R.S. & Klug, A. (1977). A crystallographic study of metal-binding to yeast phenylalanine tRNA. J. Mol. Biol. 111, 315-328.
44. Yonuschot, G., Helman, D., Mushrush, G., Woude, G.V. & Robey, G. (1978). Terbium as a solid state probe for RNA. Bioinorg. Chem. 8, 405-418.
45. Ringer, D.P., Burchett, S. & Kizer, D.E. (1978). Use of Tb(III) fluorescence enhancement to selectively monitor DNA and RNA guanine residues and their alteration by chemical modification. Biochemistry 17, 4818-4825.
46. Ringer, D.P., Howell, B.A. & Kizer, D.E. (1980). Use of terbium fluorescence enhancement as a new probe for assessing the single strand content of DNA. Anal. Biochem. 103, 337-342.
47. Fu, P.K.-L. & Turro, C. (1999). Energy transfer from nucleic acids to Tb(III): Selective emission enhancement by single DNA mismatches. J. Am. Chem. Soc. 121, 1-7.
48. Canfi, A., Bailey, M.P. & Rocks, B.F. (1989). Fluorescent terbium chelates derived from diethylenetriaminepentaacetic acid and heterocyclic compounds. Analyst 114, 1405-1406.
49. Abusaleh, A. & Meares, C.F. (1984). Excitation and de-excitation processes in lanthaide chelates bearng aromatic sidechains. Photochem. Photobiol. 39, 763-769.
50. Basu, S., et al., & Doudna, J.A. (1998). A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5, 986-992.
51. 1H NMR. Biochemistry 35, 15383-15390.
52. Katz, A.K., Glusker, J.P., Beebe, S.A. & Bock, C.W. (1996). Calcium ion coordination: A comparison with that of beryllium, magnesium, and zinc. J. Am. Chem. Soc. 118, 5752-5763.
53. Fritz, J.S., Oliver, R.T. & Pietrzyk, D.J. (1958). Chelometric titrations using an azoarsonic acid indicator. Anal. Chem. 30, 1111-1114.
54. Davanloo, P., Rosenberg, A.H., Dunn, J.J. & Studier, F.W. (1984). Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl Acad. Sci. USA 81, 2035-2039.
55. Milligan, J.F., Groebe, D.R., Witherell, G.W. & Uhlenbeck, O.C. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798.
56. Frey, S.T., et al., & Horrocks, W.D. (1994). Characterization of lanthanide complexes with a series of amide-based macrocycles, potential MRI contrast agents, using Eu(III) luminescence spectroscopy and molecular mechanics. Inorg. Chem. 33, 2882-2889.