Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1155K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (37)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Yoshinari, K.
Right arrow Articles by Taira, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yoshinari, K.
Right arrow Articles by Taira, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 8 1730-1742
© 2000 Oxford University Press

A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme

Koichi Yoshinari1,2 and Kazunari Taira1,3,3,*

1National Institute for Advanced Interdisciplinary Research, Tsukuba Science City 305-8562, Japan, 2National Institute of Bioscience and Human Technology, Tsukuba Science City 305-8566, Japan and 3Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan

We synthesized three types of 11mer substrate, namely the natural substrate S11O and the thio­substituted substrates S11SpS and S11RpS, in which the respective pro-Sp and pro-Rp oxygen atoms were replaced by sulfur, and subjected them to detailed kinetic analysis in the cleavage reaction catalyzed by a hammerhead ribozyme. In agreement with previous findings, in the presence of Mg2+ or Ca2+ ions the rate of ribozyme-catalyzed cleavage of S11SpS was as high as that of S11O, whereas the corresponding rate for S11RpS was nearly four orders of magnitude lower than that for either S11O or S11SpS. However, the rate of the ribozyme-catalyzed reaction with each of the three substrates was enhanced by Cd2+ ions. Such results have generally been taken as evidence that supports the direct interaction of the sulfur atom at the Rp position of the cleavage site with the added Cd2+ ion. However, our present analysis demonstrates that (i) the added Cd2+ ion binds at the P9 site; (ii) the bound Cd2+ ion at the P9 site replaces two Mg2+ or two Ca2+ ions, an observation that suggests a different mode of interaction with the added Cd2+ ion; and, most importantly and in contrast to the conclusion reached by other investigators, (iii) the Cd2+ ion does not interact with the sulfur atom at the Rp position of the scissile phosphate either in the ground state or in the transition state.

* To whom correspondence should be addressed at: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan. Tel: +81 3 5841 8828 or +81 298 61 3015; Fax: +81 298 61 3019; Email: taira@chembio.t.u-tokyo.ac.jp


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. E. Deweese, A. B. Burgin, and N. Osheroff
Human topoisomerase II{alpha} uses a two-metal-ion mechanism for DNA cleavage
Nucleic Acids Res., September 1, 2008; 36(15): 4883 - 4893.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Inoue, Y. Takagi, and K. Taira
Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme
Nucleic Acids Res., August 9, 2004; 32(14): 4217 - 4223.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J.-M. Zhou, D.-M. Zhou, Y. Takagi, Y. Kasai, A. Inoue, T. Baba, and K. Taira
Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme
Nucleic Acids Res., June 1, 2002; 30(11): 2374 - 2382.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Kasai, H. Shizuku, Y. Takagi, M. Warashina, and K. Taira
Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity
Nucleic Acids Res., June 1, 2002; 30(11): 2383 - 2389.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Kuwabara, M. Warashina, S. Koseki, M. Sano, J. Ohkawa, K. Nakayama, and K. Taira
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
Nucleic Acids Res., July 1, 2001; 29(13): 2780 - 2788.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Takagi, M. Warashina, W. J. Stec, K. Yoshinari, and K. Taira
SURVEY AND SUMMARY: Recent advances in the elucidation of the mechanisms of action of ribozymes
Nucleic Acids Res., May 1, 2001; 29(9): 1815 - 1834.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Kato, T. Kuwabara, M. Warashina, H. Toda, and K. Taira
Relationships between the Activities in Vitro and in Vivo of Various Kinds of Ribozyme and Their Intracellular Localization in Mammalian Cells
J. Biol. Chem., April 27, 2001; 276(18): 15378 - 15385.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.