Published online 12 February 2004
Nucleic Acids Research, 2004, Vol. 32, No. 3 916-925
© 2004 Oxford University Press
Kinetic and thermodynamic characterization of the RNA-cleaving 8-17 deoxyribozyme
Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
*To whom correspondence should be addressed. Tel: +39 0521905137; Fax: +39 0521905151; Email: alessio.peracchi{at}unipr.it
The 8-17 deoxyribozyme is a small DNA catalyst of significant applicative interest. We have analyzed the kinetic features of a well behaved 8-17 construct and determined the influence of several reaction conditions on such features, providing a basis for further exploration of the deoxyribozyme mechanism. The 8-17 bound its substrate with a rate constant 
10-fold lower than those typical for the annealing of short complementary oligonucleotides. The observed free energy of substrate binding indicates that an energetic penalty near to +7 kcal/mol is attributable to the deoxyribozyme core. Substrate cleavage required divalent metal ion cofactors, and the dependence of activity on the concentration of Mg2+, Ca2+ or Mn2+ suggests the occurrence of a single, low-specificity binding site for activating ions. The efficiency of activation correlated with the Lewis acidity of the ion cofactor, compatible with a metal-assisted deprotonation of the reactive 2'-hydroxyl group. However, alternative roles of the metal ions cannot be excluded, because those ions that are stronger Lewis acids are also capable of forming stronger interactions with ligands such as the phosphate oxygens. The apparent enthalpy of activation for the 8-17 reaction was close to the values observed for hydroxide-catalyzed and hammerhead ribozyme-catalyzed RNA cleavage.
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