Artificial zinc(II) ribonucleases: Understanding the role of two metal ions in RNA cleavage and thionucleosides as metal ion binding sites

A series of ligands containing linked 1,4,7-triazacyclononane macrocycles have been synthesised, 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-triazaclonon-1-yl)-1,10-phenanthroline (L4), and α,α′-bis(1,4,7-triazacyclonon-1-yl)- m-xylene (L5). Each ligand binds two Zn(II) ions with a very high affinity at near neutral pH under conditions of millimolar ligand and two equivalents of Zn(NO₃)₂, as determined by 1H NMR titrations.; The complexes Zn₂(L2O), Zn₂(L3), Zn₂(L4), and Zn₂(L5) are evaluated as catalysts for the cleavage of the RNA model substrate, 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP), at pH 7.61 and 25°C, and their activity is compared with that of the related mononuclear complex Zn(L1) (L1 = 1,4,7-triazacyclononane) under the same conditions. The catalytic activity of Zn₂(L3), Zn₂(L4), and Zn ₂(L5) is only 3–5 fold larger than that of Zn(L1). In contrast, the catalytic activity of Zn₂(L2O) is 120-fold greater than that of Zn(L1). These results indicate that both Zn(II) ions in Zn₂(L2O) act cooperatively in the stabilization of the transition state for HPNP cleavage at close to neutral pH.; A thorough study of the structure, solution chemistry and catalytic properties of Zn₂(L2O) and its more closely related mononuclear complex Zn(L1OH) shows that the larger catak-tic activity of Zn₂(L2O) compared with Zn(L1OH) is due to the cooperative role of the two Zn(II) ions in binding more strongly to the substrate HPNP, in facilitating the formation of the Zn(II)-bound hydroxide at close to neutral pH, and in providing additional stabilization of the rate-limiting transition state for phosphodiester cleavage.; Thionucleosides s4T and s4U are studied as ligands to anchor Cd(II) or Cu(II) to specific sites in nucleic acids. Upon deprotonation of their basic site (N3-H), s4T and s 4U bind Cd(II) with an affinity constant of K = 11000 ± 2400 M−1 and K = 2830 ± 260 M−1, respectively, while both thionucleosides reduce Cu(II) to Cu(I). Both types of interactions are consistent with the presence of a thione/thiol tautomeric equilibrium in these systems. The apparent stability constants determined for Cd(II) binding to different thiodinucleosides including, Tps4T, d-(Gps4T), d-(s4TpG), and d-(Gps4U), suggest that C d(II) binds preferentially to the thionucleoside unit, and that the presence of the second nucleoside does not markedly affect this binding.