Nucleobase catalysis in the hairpin ribozyme | Zendy

Timothy J. Wilson | Zendy; Jonathan Ouellet | Zendy; Zheng-yun Zhao | Zendy; Shinya Harusawa | Zendy; Lisa Araki | Zendy; Takushi Kurihara | Zendy; David M.J. Lilley | Zendy

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Nucleobase catalysis in the hairpin ribozyme

Author(s) -

Timothy J. Wilson,

Jonathan Ouellet,

Zheng-yun Zhao,

Shinya Harusawa,

Lisa Araki,

Takushi Kurihara,

David M.J. Lilley

Publication year - 2006

Publication title -

rna

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.037

H-Index - 171

eISSN - 1469-9001

pISSN - 1355-8382

DOI - 10.1261/rna.11706

Subject(s) - ribozyme , nucleobase , hairpin ribozyme , guanine , biology , vs ribozyme , cleavage (geology) , rna , stereochemistry , base pair , biochemistry , chemistry , nucleotide , dna , paleontology , fracture (geology) , gene

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 pK(a) 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.

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