The Dinuclear Zn(II) Complex Catalyzed Cyclization of a Series of 2-Hydroxypropyl Aryl Phosphate RNA Models: Progressive Change in Mechanism from Rate-Limiting P−O Bond Cleavage to Substrate Binding

Base moiety selectivity in cleavage of short oligoribonucleotides by di- and tri-nuclear Zn(II) complexes of azacrown-derived ligands

Cleavage of 6-mer oligoribonucleotides by the dinuclear Zn2+ complex of 1,3-bis[(1,5,9-triazacyclododecan-3-yl)oxymethyl]benzene (L1) and the trinuclear Zn2+ complex of 1,3,5-tris[(1,5,9-triazacyclododecan-3-yl)oxymethyl]benzene (L3) has been studied. The dinuclear complex cleaves at sufficiently low concentrations ([(Zn2+)2L1] < or = 0.1 mmol L(-1)) the 5'NpU3' and 5'UpN3' bonds (N = G, C, A) much more readily than the other phosphodiester bonds, but leaves the 5'UpU3' site intact. The trinuclear (Zn2+)3L3 complex, in turn, cleaves the 5'UpU3' bond more readily than any other linkages, even faster than the 5'NpU3' and 5'UpN3' sites. Somewhat unexpectedly, the 5'UpNpU3' site is cleaved only slowly by both the di- and tri-nuclear complex. The base-moiety selectivity remains qualitatively similar, though slightly less pronounced, when the hexanucleotides are closed to hairpin loops by three additional CG-pairs of 2'-O-methylribonucleotides. Phosphodiester bonds within a double helical stem are not cleaved, not even the 5'UpU3' sites. Guanine base also becomes recognized by (Zn2+)2L1 and (Zn2+)3L3, but the affinity to G is clearly lower than to U. The trinuclear cleaving agent, however, cleaves the 5'GpG3' bond only 35% less readily than the 5'UpU3' bond.

Cleavage of models for RNA mediated by a diZn(II) complex of bis[1,4-N1,N1′(1,5,9-triazacyclododecanyl)]butane in methanol and ethanol

The cleavage of seven RNA model 2-hydroxypropyl aryl phosphates (1) catalyzed by a dinuclear Zn(II) complex of bis[1,4-N1,N1′(1,5,9-triazacyclododecanyl)]butane (4) was studied in methanol and ethanol at 25 °C under pH controlled conditions. The results are compared with what was reported earlier for the dinuclear Zn(II) complex of the lower homologue bis[1,3-N1,N1′(1,5,9-triazacyclododecanyl)]propane (3). In methanol, the higher homologue exhibits saturation binding with substrates having poor aryloxy leaving groups. With good leaving groups there is an observed linear dependence of kobs versus complex concentration without saturation binding over the catalyst concentration range investigated. In ethanol, strong saturation binding between the active form of the catalyst ((RO–):Zn(II)2:4) and all substrates is observed, the results observed in both solvents being similar to what was reported for the lower (RO–):Zn(II)2:3 homologue. Energetics calculations are presented for the (RO–):Zn(II)2:4-catalyzed cleavage of each substrate in both solvents to assess the catalytic efficiency via the ΔΔG‡ for catalyst binding a transition state comprising [RO–:1]‡ or its kinetic equivalent.

Altered transition state for the reaction of an RNA model catalyzed by a dinuclear zinc(II) catalyst

The cyclization of 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group ((18)k(lg) = 1.0064 +/- 0.0009 and (15)k = 1.0002 +/- 0.0002) and that nucleophilic bond formation occurs in the rate-determining step ((18)k(nuc) = 1.0326 +/- 0.0008). In the catalyzed reaction, larger leaving group isotope effects ((18)k(lg) = 1.0113 +/- 0.0005 and (15)k = 1.0015 +/- 0.0005) and a smaller nucleophile isotope effect ((18)k(nuc) = 1.0116 +/- 0.0010) indicate a later TS with greater leaving group bond fission and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2'-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.