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Published online before print April 6, 2006, 10.1261/rna.11706
RNA (2006), 12:980-987. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 RNA Society.
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Nucleobase catalysis in the hairpin ribozyme

Timothy J. Wilson1, Jonathan Ouellet1, Zheng-yun Zhao1, Shinya Harusawa2, Lisa Araki2, Takushi Kurihara2 and David M.J. Lilley1

1 Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
2 Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan

RNA catalysis is important in the processing and translation of RNA molecules, yet the mechanisms of catalysis are still unclear in most cases. We have studied the role of nucleobase catalysis in the hairpin ribozyme, where the scissile phosphate is juxtaposed between guanine and adenine bases. We show that a modified ribozyme in which guanine 8 has been substituted by an imidazole base is active in both cleavage and ligation, with ligation rates 10-fold faster than cleavage. The rates of both reactions exhibit bell-shaped dependence on pH, with pKa values of 5.7 ± 0.1 and 7.7 ± 0.1 for cleavage and 6.1 ± 0.3 and 6.9 ± 0.3 for ligation. The data provide good evidence for general acid–base catalysis by the nucleobases.

Keywords: RNA catalysis; general acid–base; imidazole

Received January 9, 2006 ; accepted February 14, 2006.


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