Solvent Exposure Associated with Single Abasic Sites Alters the Base Sequence Dependence of Oxidation of Guanine in DNA in GG Sequence Contexts

Young Ae Lee, Zhi Liu, Peter C. Dedon, Nicholas Geacintov, Vladimir Shafirovich

Research output: Contribution to journalArticle

Abstract

The effect of exposure of guanine in double-stranded oligonucleotides to aqueous solvent during oxidation by one-electron oxidants was investigated by introducing single synthetic tetrahydrofuran-type abasic sites (Ab) either adjacent to or opposite tandem GG sequences. The selective oxidation of guanine was initiated by photoexcitation of the aromatic sensitizers riboflavin and a pyrene derivative, and by the relatively small negatively charged carbonate radical anion. The relative rates of oxidation of the 5'- and 3' side G in runs of 5'{dot operator}{dot operator}{dot operator}GG{dot operator}{dot operator}{dot operator} (evaluated by standard hot alkali treatment of the damaged DNA strand followed by high resolution gel electrophoresis of the cleavage fragments) are markedly affected by adjacent abasic sites either on the same or opposite strand. For example, in fully double-stranded DNA or one with an Ab adjacent to the 5'-G, the 5'-G/3'-G damage ratio is ≥4, but is inverted (<1.0) with the Ab adjacent to the 3'-G. These striking effects of Ab are attributed to the preferential localization of the "hole" on the most solvent-exposed guanine regardless of the size, charge, or reduction potential of the oxidizing species. Damage assessment: We have investigated the effects of solvent exposure on the oxidation of guanine in GG sequences in oligonucleotide duplexes. The results show that a single abasic site (Ab) inverts the extent of damage in GG sequences induced by one-electron oxidation when it flanks the 3' side guanine in double-stranded DNA (see histograms showing relative oxidation at G sites).

Original languageEnglish (US)
Pages (from-to)1731-1739
Number of pages9
JournalChemBioChem
Volume12
Issue number11
DOIs
StatePublished - Jul 25 2011

Fingerprint

Guanine
Oxidation
DNA
Oligonucleotides
Electrons
Riboflavin
Carbonates
Alkalies
Oxidants
Photoexcitation
Anions
Electrophoresis
Gels
Derivatives

Keywords

  • Abasic sites
  • Carbonate radicals
  • DNA
  • DNA damage
  • Oxidative damage

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry
  • Molecular Medicine
  • Molecular Biology

Cite this

Solvent Exposure Associated with Single Abasic Sites Alters the Base Sequence Dependence of Oxidation of Guanine in DNA in GG Sequence Contexts. / Lee, Young Ae; Liu, Zhi; Dedon, Peter C.; Geacintov, Nicholas; Shafirovich, Vladimir.

In: ChemBioChem, Vol. 12, No. 11, 25.07.2011, p. 1731-1739.

Research output: Contribution to journalArticle

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N2 - The effect of exposure of guanine in double-stranded oligonucleotides to aqueous solvent during oxidation by one-electron oxidants was investigated by introducing single synthetic tetrahydrofuran-type abasic sites (Ab) either adjacent to or opposite tandem GG sequences. The selective oxidation of guanine was initiated by photoexcitation of the aromatic sensitizers riboflavin and a pyrene derivative, and by the relatively small negatively charged carbonate radical anion. The relative rates of oxidation of the 5'- and 3' side G in runs of 5'{dot operator}{dot operator}{dot operator}GG{dot operator}{dot operator}{dot operator} (evaluated by standard hot alkali treatment of the damaged DNA strand followed by high resolution gel electrophoresis of the cleavage fragments) are markedly affected by adjacent abasic sites either on the same or opposite strand. For example, in fully double-stranded DNA or one with an Ab adjacent to the 5'-G, the 5'-G/3'-G damage ratio is ≥4, but is inverted (<1.0) with the Ab adjacent to the 3'-G. These striking effects of Ab are attributed to the preferential localization of the "hole" on the most solvent-exposed guanine regardless of the size, charge, or reduction potential of the oxidizing species. Damage assessment: We have investigated the effects of solvent exposure on the oxidation of guanine in GG sequences in oligonucleotide duplexes. The results show that a single abasic site (Ab) inverts the extent of damage in GG sequences induced by one-electron oxidation when it flanks the 3' side guanine in double-stranded DNA (see histograms showing relative oxidation at G sites).

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