Journal article
Differences in electrostatic potential around DNA fragments containing adenine and 8-oxo-adenine. An analysis based on regular cylindrical projection
Journal of molecular graphics & modelling, Vol.26(1), pp.282-289
07/2007
Handle:
https://hdl.handle.net/2376/101130
PMID: 17224288
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.
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Details
- Title
- Differences in electrostatic potential around DNA fragments containing adenine and 8-oxo-adenine. An analysis based on regular cylindrical projection
- Creators
- Maciej Harańczyk - Chemical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. maharan@chem.univ.gda.plJohn H MillerMaciej Gutowski
- Publication Details
- Journal of molecular graphics & modelling, Vol.26(1), pp.282-289
- Academic Unit
- Engineering and Applied Sciences (TRIC), School of
- Publisher
- United States
- Identifiers
- 99900546649701842
- Language
- English
- Resource Type
- Journal article