Hydrogen-atom abstraction from the adenine-uracil base pair.

Full Abstract

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.

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Author information

Author/s: Kim, Sunghwan (S); Meehan, Tyler (T); Schaefer, Henry F (HF);

Affiliation: Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA.

Journal and publication information

Publication Type: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.

Journal: The journal of physical chemistry. A (J Phys Chem A), published in United States. (Language: eng)

Reference: 2007-Jul; vol 111 (issue 29) : pp 6806-12

Dates: Created 2007/07/19; Completed 2007/11/27;

PMID: 17388361, status: MEDLINE (last retrieval date: 12/26/2008)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Adenine - chemistry
Base Pairing
DNA - chemistry
Hydrogen - chemistry

Associated Chemicals: Hydrogen (1333-74-0) ; Uracil (66-22-8) ; Adenine (73-24-5) ; DNA (9007-49-2)

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