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Nucleic Acids Research, 1989, Vol. 17, No. 1 355-371
© 1989

CHEMISTRY

Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding lnteractions

Naoki Sugimoto, Mary Tomka, Ryszard Kicrzek1, Philip C. Bevilacqua and Douglas H. Turner*

Department of Chemistry, University of Rochester Rochester, NY 14627, USA 1Institute of Bioorganic Chemistry, Polish Academy of Science 60-704 Poznan, Noskowskiego 12/14, Poland

*To whom correspondence should be addressed

Received July 25, 1988. Revised November 28, 1988. Accepted November 28, 1988.

The self-splicing intervening sequence from the precursor rRNA of Tetrahymena thermophila cyclizes to form a covalently closed circle. This circle can be reopened by reaction with oligonucleotides or water. The kinetics of circle opening as a function of substrate and Mg2+ concentrations have been measured for dCrU, rCdU, dCdT, and H2O addition. Comparisons with previous results for rCrU suggest: (1) the 2' OH of the 5' sugar of a dinucleoside phosphate is involved in substrate binding, and (2) the 2' OH of the 3' sugar of a dimer substrate is involved in Mg2+ binding. Evidently, the binding site for a required Mg ion is dependent on both the ribozyme and the dimer substrate.

The apparent activation energy and entropy for circle opening by hydrolysis are 31 kcal/mol and 50 eu, respectively. The large, positive activation entropy suggests a partial unfolding of the ribozyme is required for reaction.


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