The different role of high-affinity and low-affinity metal ions in cleavage by a tertiary stabilized Cis hammerhead ribozyme from tobacco ringspot virus

Oligonucleotides

Volumn 18, Issue 2, 2008, Pages 101-110

  Kisseleva, Natalia ^a   Khvorova, Anastasia ^b   Westhof, Eric ^c   Schiemann, Olav ^d   Wolfson, Alexey D ^e  

^a GOETHE UNIVERSITY   (Germany)

^b Dharmacon Inc   (United States)

^c INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^d UNIVERSITY OF ST ANDREWS   (United Kingdom)

^e UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; FRAMYCETIN; HAMMERHEAD RIBOZYME; MAGNESIUM ION; MANGANESE; METAL ION;

ARTICLE; CATALYSIS; ELECTRON SPIN RESONANCE; PLANT VIRUS; PRIORITY JOURNAL; RINGSPOT VIRUS; RNA CLEAVAGE; RNA STRUCTURE;

KOBUS; TOBACCO RINGSPOT VIRUS;

EID: 47649130326     PISSN: 15454576     EISSN: None     Source Type: Journal    
DOI: 10.1089/oli.2008.0129     Document Type: Article

References (49)

1. AUFFINGER, P., BIELECKI, L., and WESTHOF, E. (2004). Anion binding to nucleic acids. Structure 12, 379-388.
2. CANNY, M.D., and PARDI, A. (2007). Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry 46, 3826-3834.
3. CANNY, M.D., JUCKER, F.M., KELLOG, E., KHVOROVA, A., JAYASENA, S.D., and PARDI, A. (2004). Fast cleavage kinetics of a natural hammerhead ribozyme. J. Am. Chem. Soc. 126, 10848-10849.
4. CLOUET-D'ORVAL, B., STAGE, T.K., and UHLENBECK, O.C. (1995). Neomycin inhibition of the hammerhead ribozyme involves ionic interactions. Biochemistry 34, 11186-11190.
5. CURTIS, E.A., and BARTEL, D.P. (2001). The hammerhead cleavage reaction in monovalent cations. RNA 7, 546-552.
6. DAHM, S.C., DERRICK, W.B., and UHLENBECK, O.C. (1993). Evidence of the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry 32, 13040-13045.
7. DE LA PENA, M., GAGO, S., and FLORES, R. (2003). Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22, 5561-5570.
8. DUNHAM, C.M., MURRAY, J.B., and SCOTT, W.G. (2003). A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme. J. Mol. Biol. 332, 327-336.
9. FEIG, A.L. (2000). The use of manganese as a probe for elucidating the role of magnesium ions in ribozymes. In: Metal Ions in Biological Systems. A. Sigel and H. Sigel, eds. (Marcell Dekker, New York). Vol. 37, pp. 161-162.
10. FERBEYRE, G., SMITH, J.M., and CEDERGREN, R. (1998). Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell. Biol. 18, 3880-3888.
11. FORSTER, A.C., and SYMONS, R.H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active site. Cell 49, 211-220.
12. HAMMANN, C., and LILLEY, D.M. (2002). Folding and activity of the hammerhead ribozyme. ChemBioChem 3, 691-700.
13. 19F NMR. Proc. Natl. Acad. Sci. USA 98, 5503-5508.
14. HERMANN, T., and WESTHOF, E. (1998). Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J. Mol. Biol. 276, 903.
15. HERTEL, K.J., HERSCHLAG, D., and UHLENBECK, O.C. (1994). A kinetic and thermodynamic work for the hammerhead ribozyme reaction. Biochemistry 33, 3374-3385.
16. 2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity. Biochemistry 37, 18094-18101.
17. HUNSICKER, L.M., and DEROSE, V.J. (2000). Activities and relative affinities of divalent metals in unmodified and phosphorothionate-substituted hammerhead ribozymes. J. Inorg. Biochem. 80, 271-278.
18. KHVOROVA, A., LESCOUTE, A., WESTHOF, E., and JAYSENA, S.D. (2003). Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10, 708-712.
19. KIM, N-K., MURALI, A., and DEROSE, V.J. (2005). Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme. J. Am. Chem. Soc. 127, 14134-14135.
20. KISSELEVA, N., KHVOROVA, A., WESTHOF, E., and SCHIEMANN, O. (2005). Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy. RNA 11, 1-6.
21. KOMATSU, Y., YAMASHITA, Y., KAZAMA, N., and OHTSUKA, E. (1999). Induction of ribozyme activity by anti-ribozyme oligonucleotides. Nucleic Acids Symp. Ser. 42, 279-280.
22. KRONENWETT, R., HAAS, R., and SCZAKIEL, G. (1996). Kinetic selectivity of complementary nucleic acids: bcr-abl-directed antisense RNA and ribozymes. J. Mol. Biol. 259, 632-644.
23. KUIMELIS, R.G., and MCLAUGHLIN, L.W. (1996). Probing the cleavage activity of the hammer head ribozyme using analog complexes. In: Catalytic RNA. F. Eckstein and D.M.J. Lilley, eds. (Springer-Verlag, Heidelberg). Vol. 10, pp. 207.
24. KUUSELA, S., and LOENNBERG, H. (1993). Metal ions that promote the hydrolysis of nucleoside phosphoesters do not enhance intramolecular phosphate migration. J. Phys. Org. Chem. 6, 347-356.
25. LILLEY, D.M. (2003). Ribozymes - A snip too far? Nat. Struct. Biol. 10, 672-673.
26. MARTICK, M., and SCOTT, W.G. (2006). Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320.
27. MURRAY, J.B., SEYHAN, A.A., WALTER, N.G., BURKE, J.M., and SCOTT, W.G. (1998). The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5, 587-595.
28. NELSON, J.A., SHEPOTINOVSKAYA, I., and UHLENBECK, O.C. (2005). Hammerheads derived from sTRSV enhanced cleavage and ligation rate constants. Biochemistry 44, 14577-14585.
29. O'REAR, J.L., WANG, S., FEIG, A.L., BEIGELMAN, L., UHLENBECK, O.C., and HERSCHLAG, D. (2001). Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA 7, 537-545.
30. OSBORN, E.M., SCHAAK, J.E., and DEROSE, V.J. (2005). Characterization of a native hammerhead ribozyme derived from schistosomes. RNA 11, 187-196.
31. PENEDO, J.C., WILSON, T.J., JAYSENA, S.D., KHVOROVA, A., and LILLEY, D.M. (2004). Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10, 880-888.
32. PLEY, H.W., FLAHERTY, K.M., and MACKAY, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-72.
33. PRODY, G.A., BAKOS, J.T., BUZAYAN, J.M., SCHNEIDER, I.R., and BRUENING, G. (1986). Autolytic processing of dimeric plant virus satellite RNA. Science 231, 4037-4043.
34. 2+ as a probe of a divalent metal ion binding and function in enzymes and other proteins. In: Metal Ions in Biological Systems. A. Sigel and H. Sigel, eds. (Marcell Dekker, New York). Vol. 37, pp. 184.
35. ROJAS, A.A., VAZQUEZ-TELLO, A., FERBEYRE, G., VENANZETTI, F., BACHMANN, L., PAQUIN, B., SBORDONI, V., and CEDERGREN, R. (2000). Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets. Nucleic Acids Res. 28, 4037-4043.
36. ROYCHOWDHURY-SAHA, M., and BURKE, D.H. (2006). Extraordinary rates of metal ion-mediated ribozyme catalysis. RNA 12, 1845-1852.
37. ROYCHOWDHURY-SAHA, M., and BURKE, D.H. (2007). Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme. RNA 13, 841-848.
38. RUFFNER, D.E., STORMO, G.D., and UHLENBECK, O.C. (1990). Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695-10702.
39. SAKSMERPROME, V., ROYCHOWDHURY-SAHA, M., JAYASENA, S., KHVOROVA, A., and BURKE, D. (2004). Artificial tertiary motif stabilize trans-cleaving hammerhead ribozyme under conditions of submillimolar divalent ions and high temperatures. RNA 10, 1916-1924.
40. 2+ binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding. ChemBioChem 4, 1057-1065.
41. SCOTT, W.G., FINCH, J.T., and KLUG, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81, 991-1002.
42. SCOTT, W.G., MURRAY, J.B., ARNOLD, J.R.P., STODDARD, B.L., and KLUG, A. (1996). Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065-2069.
43. SINGH, K.K., PARWARESCH, R., and KRUPP, G. (1999). Rapid kinetic characterization of hammerhead ribozymes by real-time monitoring of fluorescence resonance energy transfer (FRET). RNA 5, 1348-1356.
44. STAGE, T.K., HERTEL, K.J., and UHLENBECK, O.C. (1995). Inhibition of the hammerhead ribozyme by neomycin. RNA 1, 95-101.
45. STAGE-ZIMMERMANN, T.K. and UHLENBECK, O.C. (1998). Hammerhead ribozyme kinetics. RNA 4, 875-889.
46. SYMONS, R.H. (1992). Small catalytic RNAs. Annu. Rev. Biochem. 61, 641-671.
47. TAKAGI, Y., INOUE, A., and TAIRA, K. (2004). Analysis on a cooperative pathway involving multiple cations in hammerhead reactions. J. Am. Chem. Soc. 126, 12856-12864.
48. UHLENBECK, O.C. (1987). A small catalytic oligoribonucleotide. Nature 328, 596-600.
49. ZHANG, Y., and EPSTEIN, L.M. (1996). Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians. Gene 172, 183-190.