Combination of a dinuclear Zn2+ complex and a medium effect exerts a 10(12)-fold rate enhancement of cleavage of an RNA and DNA model system

J Am Chem Soc. 2006 Dec 20;128(50):16398-405. doi: 10.1021/ja0651714.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cations, Divalent / chemistry
  • Cyclization
  • DNA / chemistry*
  • Kinetics
  • Methane / chemistry
  • Models, Biological*
  • Molecular Structure
  • RNA / chemistry*
  • Zinc / chemistry*

Substances

  • Cations, Divalent
  • RNA
  • DNA
  • Zinc
  • Methane