Mechanisms of oxidation of guanine in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate

Young Ae Lee, Byeong Hwa Yun, Seog K. Kim, Yelena Margolin, Peter C. Dedon, Nicholas Geacintov, Vladimir Shafirovich

Research output: Contribution to journalArticle

Abstract

Peroxynitrite is produced during inflammation and combines rapidly with carbon dioxide to yield the unstable nitrosoperoxycarbonate, which decomposes (in part) to CO3̇- and ̇NO2 radicals. The CO3̇- radicals oxidize guanine bases in DNA through a one-electron transfer reaction process that ultimately results in the formation of stable guanine oxidation products. Here we have explored these mechanisms, starting with a spectroscopic study of the kinetics of electron transfer from 20-22mer double-stranded oligonucleotides to CO3 ̇- radicals, together with the effects of base sequence on the formation of the end-products in runs of one, two, or three contiguous guanines. The distributions of these alkali-labile lesions were determined by gel electrophoresis methods. The cascade of events was initiated through the use of 308 nm XeCl excimer laser pulses to generate CO3̇- radicals by an established method based on the photodissociation of persulfate to sulfate radicals and the oxidation of bicarbonate. Although the Saito model (Saito et al., J. Am. Chem. Soc. 1995, 117, 6406-6407) predicts relative ease of one-electron oxidations in DNA, following the trend 5′- ⋯GGG⋯ > 5′⋯GG⋯ > 5′-G′, we found that the rate constants for CO3̇-mediated oxidation of guanines in these sequence contexts (k5) showed only small variation within a narrow range [(1.5-3.0) × 107M -1S-1]. In contrast, the distributions of the end-products are dependent on the base sequence context and are higher at the 5′-G in 5′-⋯GG⋯ sequences and at the first two 5′-guanines in the 5′-⋯GGG⋯ sequences. These effects are attributed to a combination of initial hole distributions among the contiguous guanines and the subsequent differences in chemical reaction yields at each guanine. The lack of dependence of k5 on sequence context indicates that the one-electron oxidation of guanine in DNA by CO3̇- radicals occurs by an inner-sphere mechanism.

Original languageEnglish (US)
Pages (from-to)4571-4581
Number of pages11
JournalChemistry - A European Journal
Volume13
Issue number16
DOIs
StatePublished - 2007

Fingerprint

Carbonates
Guanine
Anions
DNA
Negative ions
Decomposition
Oxidation
Electrons
Photodissociation
Oligonucleotides
Excimer lasers
Electrophoresis
Chemical reactions
Laser pulses
Rate constants
Carbon dioxide
Gels
Peroxynitrous Acid
nitrosoperoxycarbonate
Alkalies

Keywords

  • DNA
  • Hole transfer
  • Kinetics
  • Oxidative damage
  • Radicals

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Mechanisms of oxidation of guanine in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate. / Lee, Young Ae; Yun, Byeong Hwa; Kim, Seog K.; Margolin, Yelena; Dedon, Peter C.; Geacintov, Nicholas; Shafirovich, Vladimir.

In: Chemistry - A European Journal, Vol. 13, No. 16, 2007, p. 4571-4581.

Research output: Contribution to journalArticle

Lee, Young Ae ; Yun, Byeong Hwa ; Kim, Seog K. ; Margolin, Yelena ; Dedon, Peter C. ; Geacintov, Nicholas ; Shafirovich, Vladimir. / Mechanisms of oxidation of guanine in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate. In: Chemistry - A European Journal. 2007 ; Vol. 13, No. 16. pp. 4571-4581.
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AB - Peroxynitrite is produced during inflammation and combines rapidly with carbon dioxide to yield the unstable nitrosoperoxycarbonate, which decomposes (in part) to CO3̇- and ̇NO2 radicals. The CO3̇- radicals oxidize guanine bases in DNA through a one-electron transfer reaction process that ultimately results in the formation of stable guanine oxidation products. Here we have explored these mechanisms, starting with a spectroscopic study of the kinetics of electron transfer from 20-22mer double-stranded oligonucleotides to CO3 ̇- radicals, together with the effects of base sequence on the formation of the end-products in runs of one, two, or three contiguous guanines. The distributions of these alkali-labile lesions were determined by gel electrophoresis methods. The cascade of events was initiated through the use of 308 nm XeCl excimer laser pulses to generate CO3̇- radicals by an established method based on the photodissociation of persulfate to sulfate radicals and the oxidation of bicarbonate. Although the Saito model (Saito et al., J. Am. Chem. Soc. 1995, 117, 6406-6407) predicts relative ease of one-electron oxidations in DNA, following the trend 5′- ⋯GGG⋯ > 5′⋯GG⋯ > 5′-G′, we found that the rate constants for CO3̇-mediated oxidation of guanines in these sequence contexts (k5) showed only small variation within a narrow range [(1.5-3.0) × 107M -1S-1]. In contrast, the distributions of the end-products are dependent on the base sequence context and are higher at the 5′-G in 5′-⋯GG⋯ sequences and at the first two 5′-guanines in the 5′-⋯GGG⋯ sequences. These effects are attributed to a combination of initial hole distributions among the contiguous guanines and the subsequent differences in chemical reaction yields at each guanine. The lack of dependence of k5 on sequence context indicates that the one-electron oxidation of guanine in DNA by CO3̇- radicals occurs by an inner-sphere mechanism.

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