Cooperativity between Metal Ions in the Cleavage of Phosphate Diesters and RNA by Dinuclear Zn(II) Catalysts

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Abstract
A series of ligands containing linked 1,4,7-triazacyclononane macrocycles are studied for the preparation of dinuclear Zn(II) complexes including 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (L2OH), 1,5-bis(1,4,7-triazacyclonon-1-yl)pentane (L3), 2,9-bis(1-methyl-1,4,7-triazacyclonon-1-yl)-1,10-phenanthroline (L4), and α,α‘-bis(1,4,7-triazacyclonon-1-yl)-m-xylene (L5). The titration of these ligands with Zn(NO3)2 was monitored by 1H NMR. Each ligand was found to bind two Zn(II) ions with a very high affinity at near neutral pH under conditions of millimolar ligand and 2 equiv of Zn(NO3)2. In contrast, a stable mononuclear complex was formed in solutions containing 5.0 mM L2OH and 1 equiv of Zn(NO3)2. 1H and 13C NMR spectral data are consistent with formation of a highly symmetric mononuclear complex Zn(L2OH) in which a Zn(II) ion is sandwiched between two triazacyclononane units. The second-order rate constant kZn for the cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP) at pH 7.6 and 25 °C catalyzed by Zn2(L2O) is 120-fold larger than that for the reaction catalyzed by the closely related mononuclear complex Zn(L1) (L1 = 1,4,7-triazacyclononane). By comparison, the observation that the values of kZn determined under similar reaction conditions for cleavage of HPNP catalyzed by the other Zn(II) dinuclear complexes are only 3−5-fold larger than values of kZn for catalysis by Zn(L1) provides strong evidence that the two Zn(II) cations in Zn2(L2O) act cooperatively in the stabilization of the transition state for cleavage of HPNP. The extent of cleavage of an oligoribonucleotide by Zn(L1), Zn2(L5), and Zn2(L2O) at pH 7.5 and 37 °C after 24 h incubation is 4,10, and 90%. The rationale for the observed differences in catalytic activity of these dinuclear Zn(II) complexes is discussed in terms of the mechanism of RNA cleavage and the structure and speciation of these complexes in solution.