Differences in electrostatic potential around DNA fragments containing adenine and 8-oxo-adenine. An analysis based on regular cylindrical projection

Maciej Harańczyk, John H. Miller, Maciej Gutowski

Research output: Contribution to journalArticle

4 Citations (Scopus)

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(d,p) basis sets. The "intact" DNA fragment contained adenine in the middle layer, while the "damaged" fragment had the adenine replaced with 8-oxo-adenine. The electrostatic potential around these DNA fragments was projected on a cylindrical surface around the double helix. The two-dimensional maps of EP of the intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-adenine (8oA). It was found that distortions of a phosphate group neighboring 8oA and displacements of the accompanying countercation are clearly reflected in the EP maps. © 2007 Elsevier Inc. All rights reserved.

Original languageEnglish
Pages (from-to)282-289
Number of pages8
JournalJournal of Molecular Graphics and Modelling
Volume26
Issue number1
DOIs
Publication statusPublished - Jul 2007

Keywords

  • 8-Oxo-adenine
  • Electrostatic potential
  • Oxidative DNA damage

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