Differences in electrostatic potential around DNA fragments containing guanine and 8-oxo-guanine

Maciej Harańczyk, Maciej Gutowski

Research output: Contribution to journalArticle

Abstract

Changes of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large-scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The "intact" DNA fragment contained guanine in the middle layer, while the "damaged" fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps. © 2006 Springer-Verlag.

Original languageEnglish
Pages (from-to)291-296
Number of pages6
JournalTheoretical Chemistry Accounts
Volume117
Issue number2
DOIs
Publication statusPublished - Feb 2007

Fingerprint

Guanine
Electrostatics
DNA
Nucleotides
Chemical modification
Structural optimization
Density functional theory
Phosphates
Molecules

Keywords

  • 8-oxo-guanine
  • DNA damage
  • Electrostatic potential

Cite this

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abstract = "Changes of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large-scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The {"}intact{"} DNA fragment contained guanine in the middle layer, while the {"}damaged{"} fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps. {\circledC} 2006 Springer-Verlag.",
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Differences in electrostatic potential around DNA fragments containing guanine and 8-oxo-guanine. / Harańczyk, Maciej; Gutowski, Maciej.

In: Theoretical Chemistry Accounts, Vol. 117, No. 2, 02.2007, p. 291-296.

Research output: Contribution to journalArticle

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AU - Harańczyk, Maciej

AU - Gutowski, Maciej

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