Kinetic and thermodynamic analysis of the hydrolytic ring-opening of the malondialdehyde-deoxyguanosine adduct, 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)- pyrimido[1,2-alpha]purin-10(3H)-one

J Am Chem Soc. 2004 Jul 7;126(26):8237-43. doi: 10.1021/ja040009r.

Abstract

3-(2'-Deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3H)-one (M1dG) is the major reaction product of deoxyguanosine with malondialdehyde or base propenals. M1dG undergoes hydrolytic ring-opening to N2-oxopropenyl-deoxyguanosine (N2OPdG) under basic conditions. We report that ring-opening of M1dG as a nucleoside or in oligonucleotides is a reversible second-order reaction with hydroxide ion. NMR and UV analysis revealed N2OPdG(-) to be the only product of M1dG ring-opening in basic solution. The rate constant for reaction of M1dG with hydroxide is 3.8 M(-1) s(-1), and the equilibrium constant is calculated to be 2.1 +/- 0.3 x 10(4) M(-1) at 25 degrees C. Equilibrium constants determined by spectroscopic analysis of the reaction end-point or by thermodynamic analysis of rate constants determined over a range of temperatures yielded a value 2.5 +/- 0.2 x 10(4) M(-1). Kinetic analysis of ring-opening of M1dG in oligonucleotides indicated the rate constant for ring-opening is decreased 10-fold compared to that in the nucleoside. Flanking purines or pyrimidines did not significantly alter the rate constants for ring-opening, but purines flanking M1dG enhanced the rate constant for the reverse reaction. A mechanism is proposed for ring-opening of M1dG under basic conditions and a role is proposed for duplex DNA in accelerating the rate of ring-opening of M1dG at neutral pH.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA Adducts / chemistry*
  • Deoxyguanosine / chemistry*
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Malondialdehyde / chemistry*
  • Models, Chemical
  • Molecular Structure
  • Oligonucleotides / chemistry
  • Oligosaccharides / chemistry*
  • Purine Nucleosides*
  • Purines / chemistry*
  • Pyrimidines / chemistry*
  • Spectrophotometry, Ultraviolet
  • Thermodynamics

Substances

  • 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido(1,2-alpha)purin-10(3H)-one
  • DNA Adducts
  • Oligonucleotides
  • Oligosaccharides
  • Purine Nucleosides
  • Purines
  • Pyrimidines
  • Malondialdehyde
  • Deoxyguanosine