Combination of a Dinuclear Zn²⁺Complex and a Medium Effect Exerts a 10¹²-Fold Rate Enhancement of Cleavage of an RNA and DNA Model System

Abstract

The catalytic ability of a dinuclear Zn2+ complex of 1,3-bis-N1-(1,5,9-triazacyclododecyl)propane (3) in promoting the cleavage of an RNA model, 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP, 1), and a DNA model, methyl p-nitrophenyl phosphate (MNPP, 4), was studied in methanol solution in the presence of added CH3O- at 25 degrees C. The di-Zn2+ complex (Zn2 :3), in the presence of 1 equiv of added methoxide, exhibits a second-order rate constant of (2.75 +/- 0.10) x 10(5) M(-1) s(-1) for the reaction with 1 at s(s)pH 9.5, this being 10(8)-fold larger than the k2 value for the CH3O- promoted reaction (kOCH3 = (2.56 +/- 0.16) x 10(-3) M(-1) s(-1)). The complex is also active toward the DNA model 4, exhibiting Michaelis-Menten kinetics with a KM and kmax of 0.37 +/- 0.07 mM and (4.1 +/- 0.3) x 10(-2) s(-1), respectively. Relative to the background reactions at s(s)pH 9.5, Zn2 :3 accelerates cleavage of each phosphate diester by a remarkable factor of 1012-fold. A kinetic scheme common to both substrates is discussed. The study shows that a simple model system comprising a dinuclear Zn2+ complex and a medium effect of the alcohol solvent achieves a catalytic reactivity that approaches enzymatic rates and is well beyond anything seen to date in water for the cleavage of these phosphate diesters.

Efficient syntheses of artificial nucleases containing mono-, di- and tri-[12]aneN3 ligating units through click chemistry

“…The systems containing one or more [12]aneN 3 units have shown prominent results in the detailed mechanism studies and excellent catalytic performance [16][17][18][19][20]. Recently we found that the dinuclear zinc(II) complex of 1,3-bis-[12]aneN 3 -propane accelerates the cleavage of model phosphate diesters by a remarkable factor of 10 12 -fold, when compared to the background reactions [21,22].With the above consideration, we report here on the syntheses and characterization of artificial nucleases containing mono-, di-and trinucleating [12]aneN 3 ligating units through click reactions between propargyl modified [12]aneN 3 and various azides.Our syntheses started from tri-tert-butyl-3-hydroxy-1,5,9-triazacyclododecane-1,5,9-tricarboxylate 1, which was prepared according to the literature reported by Lönnberg [16]. The synthetic route of the propargyl modified [12]aneN 3 compound, tri-tert-butyl-3-(prop-2-ynyloxy)-1,5,9-triazacyclododecane-1,5,9-tricarboxylate 2 is outlined in Scheme 1.…”

“…The systems containing one or more [12]aneN 3 units have shown prominent results in the detailed mechanism studies and excellent catalytic performance [16][17][18][19][20]. Recently we found that the dinuclear zinc(II) complex of 1,3-bis- [12]aneN 3 -propane accelerates the cleavage of model phosphate diesters by a remarkable factor of 10 12 -fold, when compared to the background reactions [21,22].…”

“…by mixing ligand, base, and metal salts in appropriate ratio [21,22]. The catalytic activities of zinc(II) and copper complexes on the methanolysis of phosphate diester, 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP), which is often used as model compound of RNA (Scheme 3), were tested [29].…”

“…ii) Removal of Boc protecting groups through hydrolysis: The above prepared compounds were dissolved in MeOH (20 ml), and concentrated HCl (1.0 ml) was added to the above solution. The kinetics of methanolysis of HPNPP promoted by zinc(II) and copper complexes were performed following the procedure in literature [21][22] at the self-buffered condition with HPNPP at 4.0 × 10 − 5 mol dm − 3 and temperature at 25 ± 0.1°C. The stock solutions of the complexes at 1 × 10 − 3 mol dm − 3 were prepared in pure methanol by sequential addition of aliquots of stock solutions of sodium methoxide, ligand and Zn(CF 3 SO 3 )2 such that the relative amounts were 0.5:1.0:1.0, 1.0:1.0:2.0, and 1.5:1.0:3.0 for mononuclear, dinuclear, and trinuclear complexes, respectively.…”

The impact of the second coordination sphere in phosphatase model complexes

“…108,109 Thus, the capacity of this model complex However, it should not be underestimated that in addition to specific chemical features, the remarkable catalytic activity of phosphatase enzymes may also derive from the polarity and the steric demand of the environment of the active site. 273 It has been suggested that the catalysis of enzymes is promoted by binding of the substrate in hydrophobic pockets with an apparent dielectric constant much lower than the surrounding water. In this way, both the equilibrium for proton transfer reactions is shifted and the strengths of hydrogen bonds, involving the substrate binding and the transition state stabilization, are changed.…”