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Nucleic Acids Research, 2000, Vol. 28, No. 17 3269-3277
© 2000 Oxford University Press

Structure–function relationships of two closely related group IC3 intron ribozymes from Azoarcus and Synechococcus pre-tRNA

Yoshiya Ikawa, Daisuke Naito, Hideaki Shiraishi and Tan Inoue*

Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan

The two group IC3 pre-tRNA introns from Azoarcus and Synechococcus share very analogous secondary structures. They are small group I ribozymes that possess only two peripheral domains, P2 and P9. However, the 3'-splice site hydrolysis activity of the Synechococcus ribozyme critically depends on P2 whereas that of Azoarcus does not, indicating that the structure–function relationships of the two ribozymes are strikingly different despite their structural resemblance. To identify the element(s) that determines the catalytic properties of these ribozymes, we undertook analyses of chimeric ribozymes prepared by swapping their structural elements. We found that the difference can be attributed to a small number of nucleotides within the conserved core region. Further analysis by employing in vitro selection revealed that a base triple interaction (P4bp3 x J6/7-2) is a critical element for determining activity and suggests the existence of a novel base quintuple involving the base triple P4bp5 x J8/7-5.

* To whom correspondence should be addressed. Tel: +81 075 753 3995; Fax: +81 075 753 3996; Email: tan@kuchem.kyoto-u.ac.jp


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