Cleavage of a RNA analog containing uridine by a bifunctional dinuclear Zn(II) catalyst

The macrocyclic ligand, 1,4-bis((1-oxa-4,7,10-triazacyclododecan-7-yl)methyl)benzene (L1) is prepared. L1 binds two Zn(II) ions at neutral pH to form Zn2(L1) as studied by using pH-potentiometric titrations. Zn2(L1) binds two uridines at pH 7.0, I = 0.100 M (NaCl) and the mononuclear analog Zn(L2) (L2 = 1-oxa-4,7,10-triazacyclododecane) binds a single uridine; dissociation constants for both complexes are in the millimolar range. Both complexes promote the cleavage of a simple RNA analog lacking a nucleobase (HpPNP = 2-hydroxypropyl-4-nitrophenylphosphate), and a uridine containing RNA analog UpPNP (uridine-3′-4-nitrophenylphosphate). Plots of the first-order rate constant for cleavage of HpPNP as a function of Zn(L2) concentration from 0.5 mM to 20.0 mM are linear, consistent with weak complexation to substrate Kd > 20 mM. In contrast, first-order rate constants for cleavage of UpPNP by Zn(L2) or Zn2(L1) over similar concentration ranges exhibit a downward curvature, consistent with the formation of a complex between catalyst and UpPNP. Comparison of second-order rate constants (k2 = kcat/Kd) shows that the dinuclear complex Zn2(L1) is a better catalyst than Zn(L2) for both HpPNP and UpPNP cleavage.