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Issue 36, 2012
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On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium

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Abstract

Different deprotonation paths of the radical cation formed by one-electron oxidation of 2′-deoxyguanosine (2dG) sites in DNA have been studied using Density Functional Theory (M05-2X/6-31+G(d,p)) and ONIOM methodology (M05-2X/6-31+G(d,p):PM6) in conjunction with the SMD model to include the solvent effects. Models of increased complexity have been used ranging from the isolated nucleoside to a three unit double-stranded oligomer including the sugar units, the base pairing with cytidine, and the phosphate linkage. The reported results correspond to aqueous solution, at room temperature, and pH = 7.4. Under such conditions it was found that the proton transfer (PT) within the base pair is a minor path compared to the PT between the base pair and the surrounding water. It was also found that the deprotonation of ground-state 2dG˙+ sites mainly yields C centered radicals in the sugar unit, with the largest populations corresponding to C4′˙ and C5′˙, followed by C3′˙. The different aspects of the presented theoretical study have been validated with experimental results.

Graphical abstract: On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium

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Article information


Submitted
13 Mar 2012
Accepted
30 Apr 2012
First published
30 Apr 2012

Phys. Chem. Chem. Phys., 2012,14, 12476-12484
Article type
Paper

On the evolution of one-electron-oxidized deoxyguanosine in damaged DNA under physiological conditions: a DFT and ONIOM study on proton transfer and equilibrium

A. Galano and J. R. Alvarez-Idaboy, Phys. Chem. Chem. Phys., 2012, 14, 12476
DOI: 10.1039/C2CP40799J

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