Thermodynamic and Activation Parameters for Binding of a Pyrene-Labeled Substrate by the Tetrahymena Ribozyme: Docking Is Not Diffusion-Controlled and Is Driven by a Favorable Entropy Change

Yi Li, Philip C. Bevilacqua, David Mathews, Douglas H. Turner

Research output: Contribution to journalArticlepeer-review

51 Scopus citations

Abstract

Association and dissociation rates for the pyrene-(pyr)-labeled oligoribonucleotide substrate pyrCUCU binding to the L-21 Seal group I ribozyme are reported as a function of temperature. Combined with thermodynamic parameters for binding of pyrCUCU to rGGAGAA, the results allow calculation of the activation and thermodynamic parameters for docking of pyrCUCU into the catalytic core of the ribozyme. The activation enthalpy for docking is 22 keal/mol, much larger than the ~4 keal/mol expected for a diffusion-controlled process. Thus, docking is not diffusion-controlled. The activation and equilibrium entropies for docking are favorable at 21 and 37 eu, respectively. The results suggest the rate-limiting step and the driving force for docking may involve desolvation of RNA functional groups or of Mg2+ ions.

Original languageEnglish (US)
Pages (from-to)14394-14399
Number of pages6
JournalBiochemistry
Volume34
Issue number44
DOIs
StatePublished - Nov 1995

All Science Journal Classification (ASJC) codes

  • Biochemistry

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