Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 6 August 1993:
Vol. 261. no. 5122, pp. 709 - 714
DOI: 10.1126/science.7688142

Articles

Science, Vol 261, Issue 5122, 709-714
Copyright © 1993 by American Association for the Advancement of Science


articles

Ribozymes: a distinct class of metalloenzymes

AM Pyle

Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, New York, NY 10032.

Ribozymes are an important new class of metalloenzymes that have an unlikely feature: they are made entirely of ribonucleic acid (RNA). Metal ions are essential for efficient chemical catalysis by ribozymes and are often required for the stabilization of ribozyme structure. Most ribozymes catalyze reactions at phosphorus centers through one of two major mechanistic pathways, and reaction has been observed at carbon centers. Creative experiments have revealed the position of metal ions in the active site of two ribozymes. The exploitation of variable metal geometry and reactivity has expanded ribozyme chemistry and has facilitated the application of in vitro selection for the creation of novel ribozymes.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method.
D. Jaikaran, M. D. Smith, R. Mehdizadeh, J. Olive, and R. A. Collins (2008)
RNA 14, 938-949
   Abstract »    Full Text »    PDF »
The electrostatic characteristics of G{middle dot}U wobble base pairs.
D. Xu, T. Landon, N. L. Greenbaum, and M. O. Fenley (2007)
Nucleic Acids Res. 35, 3836-3847
   Abstract »    Full Text »    PDF »
MeRNA: a database of metal ion binding sites in RNA structures.
L. R. Stefan, R. Zhang, A. G. Levitan, D. K. Hendrix, S. E. Brenner, and S. R. Holbrook (2006)
Nucleic Acids Res. 34, D131-D134
   Abstract »    Full Text »    PDF »
In vitro selection, characterization, and application of deoxyribozymes that cleave RNA.
S. K. Silverman (2005)
Nucleic Acids Res. 33, 6151-6163
   Abstract »    Full Text »    PDF »
Substrate specificity and reaction kinetics of an X-motif ribozyme.
D. LAZAREV, I. PUSKARZ, and R. R. BREAKER (2003)
RNA 9, 688-697
   Abstract »    Full Text »    PDF »
Specific Cleavage of Hepatitis C Virus RNA Genome by Human RNase P.
A. Nadal, M. Martell, J. R. Lytle, A. J. Lyons, H. D. Robertson, B. Cabot, J. I. Esteban, R. Esteban, J. Guardia, and J. Gomez (2002)
J. Biol. Chem. 277, 30606-30613
   Abstract »    Full Text »    PDF »
Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme.
J.-M. Zhou, D.-M. Zhou, Y. Takagi, Y. Kasai, A. Inoue, T. Baba, and K. Taira (2002)
Nucleic Acids Res. 30, 2374-2382
   Abstract »    Full Text »    PDF »
Structural Insights into Group II Intron Catalysis and Branch-Site Selection.
L. Zhang and J. A. Doudna (2002)
Science 295, 2084-2088
   Abstract »    Full Text »    PDF »
Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.
C. Burkhardt and M. Zacharias (2001)
Nucleic Acids Res. 29, 3910-3918
   Abstract »    Full Text »    PDF »
Significantly higher activity of a cytoplasmic hammerhead ribozyme than a corresponding nuclear counterpart: engineered tRNAs with an extended 3' end can be exported efficiently and specifically to the cytoplasm in mammalian cells.
T. Kuwabara, M. Warashina, S. Koseki, M. Sano, J. Ohkawa, K. Nakayama, and K. Taira (2001)
Nucleic Acids Res. 29, 2780-2788
   Abstract »    Full Text »    PDF »
SURVEY AND SUMMARY: Recent advances in the elucidation of the mechanisms of action of ribozymes.
Y. Takagi, M. Warashina, W. J. Stec, K. Yoshinari, and K. Taira (2001)
Nucleic Acids Res. 29, 1815-1834
   Abstract »    Full Text »    PDF »
Reversible Unfolding of Single RNA Molecules by Mechanical Force.
J. Liphardt, B. Onoa, S. B. Smith, I. Tinoco Jr., and C. Bustamante (2001)
Science 292, 733-737
   Abstract »    Full Text »
Quantitative studies of Mn2+-promoted specific and non-specific cleavages of a large RNA: Mn2+-GAAA ribozymes and the evolution of small ribozymes.
T.-C. Kuo and D. L. Herrin (2000)
Nucleic Acids Res. 28, 4197-4206
   Abstract »    Full Text »    PDF »
A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme.
K. Yoshinari and K. Taira (2000)
Nucleic Acids Res. 28, 1730-1742
   Abstract »    Full Text »    PDF »
In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.
J. Li, W. Zheng, A. H. Kwon, and Y. Lu (2000)
Nucleic Acids Res. 28, 481-488
   Abstract »    Full Text »    PDF »
A small nucleolar RNA:ribozyme hybrid cleaves a nucleolar RNA target in vivo with near-perfect efficiency.
D. A. Samarsky, G. Ferbeyre, E. Bertrand, R. H. Singer, R. Cedergren, and M. J. Fournier (1999)
PNAS 96, 6609-6614
   Abstract »    Full Text »    PDF »
Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics.
J. Pan, D. Thirumalai, and S. A. Woodson (1999)
PNAS 96, 6149-6154
   Abstract »    Full Text »    PDF »
Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution.
L. F. Landweber and I. D. Pokrovskaya (1999)
PNAS 96, 173-178
   Abstract »    Full Text »    PDF »
Catalytic Cleavage of the Androgen Receptor Messenger RNA and Functional Inhibition of Androgen Receptor Activity by a Hammerhead Ribozyme.
S. Chen, C. S. Song, Y. Lavrovsky, B. Bi*, B. Chatterjee, and A. K. Roy (1998)
Mol. Endocrinol. 12, 1558-1566
   Abstract »    Full Text »
RNA folding causes secondary structure rearrangement.
M. Wu and I. Tinoco Jr. (1998)
PNAS 95, 11555-11560
   Abstract »    Full Text »    PDF »
Nucleic Acid Therapeutics: State of the Art and Future Prospects.
A. M. Gewirtz, D. L. Sokol, and M. Z. Ratajczak (1998)
Blood 92, 712-736
   Full Text »    PDF »
Nucleic acid enzymes: Playing with a fuller deck.
G. F. Joyce (1998)
PNAS 95, 5845-5847
   Full Text »    PDF »
An amino acid as a cofactor for a catalytic polynucleotide.
A. Roth and R. R. Breaker (1998)
PNAS 95, 6027-6031
   Abstract »    Full Text »    PDF »
Explanation by the double-metal-ion mechanism of catalysis for the differential metal ion effects on the cleavage rates of 5'-oxy and 5'-thio substrates by a hammerhead ribozyme.
D.-M. Zhou, L.-H. Zhang, and K. Taira (1997)
PNAS 94, 14343-14348
   Abstract »    Full Text »    PDF »
In vitro selection of self-cleaving RNAs with a low pH optimum.
V. K. Jayasena and L. Gold (1997)
PNAS 94, 10612-10617
   Abstract »    Full Text »    PDF »
Ribosomal Binding Site of Release Factors RF1 and RF2. A NEW TRANSLATIONAL TERMINATION ASSAY IN VITRO.
G. Grentzmann and P. J. Kelly (1997)
J. Biol. Chem. 272, 12300-12304
   Abstract »    Full Text »    PDF »
Discrimination of a single base change in a ribozyme using the gene for dihydrofolate reductase as a selective marker in Escherichia coli.
S. Fujita, T. Koguma, J. Ohkawa, K. Mori, T. Kohda, H. Kise, S. Nishikawa, M. Iwakura, and K. Taira (1997)
PNAS 94, 391-396
   Abstract »    Full Text »    PDF »
Ribonuclease P of Tetrahymena thermophila.
H. L. True and D. W. Celander (1996)
J. Biol. Chem. 271, 16559-16566
   Abstract »    Full Text »    PDF »
Magnesium-mediated Conversion of an Inactive Form of a Hammerhead Ribozyme to an Active Complex with Its Substrate.
M. Orita, R. Vinayak, A. Andrus, M. Warashina, A. Chiba, H. Kaniwa, F. Nishikawa, S. Nishikawa, and K. Taira (1996)
J. Biol. Chem. 271, 9447-9454
   Abstract »    Full Text »    PDF »
Structurally complex and highly active RNA ligases derived from random RNA sequences.
E. Ekland, J. Szostak, and D. Bartel (1995)
Science 269, 364-370
   Abstract »    PDF »
Prebiotic synthesis of 5-substituted uracils: a bridge between the RNA world and the DNA-protein world.
M. Robertson and S. Miller (1995)
Science 268, 702-705
   Abstract »    PDF »
Kinetic intermediates in RNA folding.
P. Zarrinkar and Williamson JR (1994)
Science 265, 918-924
   Abstract »    PDF »
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
H Pelletier, M. Sawaya, A Kumar, S. Wilson, and J Kraut (1994)
Science 264, 1891-1903
   Abstract »    PDF »
Guides to the heart of the spliceosome.
J. Wise (1993)
Science 262, 1978-1979
   PDF »
Bioinorganic chemistry: a maturing frontier.
S. Lippard (1993)
Science 261, 699-700
   PDF »



ADVERTISEMENT
Click Me!

ADVERTISEMENT

To Advertise     Find Products


Science. ISSN 0036-8075 (print), 1095-9203 (online)