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World J Clin Oncol. Nov 10, 2010; 1(1): 12-17
Published online Nov 10, 2010. doi: 10.5306/wjco.v1.i1.12
Molecular mechanism of base pairing infidelity during DNA duplication upon one-electron oxidation
Jóhannes Reynisson
Jóhannes Reynisson, Department of Chemistry and Auckland Bioengineering Institute, The University of Auckland, Auckland 1142, New Zealand
Author contributions: Reynisson J solely contributed to this paper.
Correspondence to: Dr. Jóhannes Reynisson, Department of Chemistry and Auckland Bioengineering Institute, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. j.reynisson@auckland.ac.nz
Telephone: +64-9-3737599 Fax: +64-9-3737422
Received: April 16, 2010
Revised: September 21, 2010
Accepted: September 28, 2010
Published online: November 10, 2010
Abstract

The guanine radical cation (G•+) is formed by one-electron oxidation from its parent guanine (G). G•+ is rapidly deprotonated in the aqueous phase resulting in the formation of the neutral guanine radical [G(-H)]. The loss of proton occurs at the N1 nitrogen, which is involved in the classical Watson-Crick base pairing with cytosine (C). Employing the density functional theory (DFT), it has been observed that a new shifted base pairing configuration is formed between G(-H) and C constituting only two hydrogen bonds after deprotonation occurs. Using the DFT method, G(-H) was paired with thymine (T), adenine (A) and G revealing substantial binding energies comparable to those of classical G-C and A-T base pairs. Hence, G(-H) does not display any particular specificity for C compared to the other bases. Taking into account the long lifetime of the G(-H) radical in the DNA helix (5 s) and the rapid duplication rate of DNA during mitosis/meiosis (5-500 bases per s), G(-H) can pair promiscuously leading to errors in the duplication process. This scenario constitutes a new mechanism which explains how one-electron oxidation of the DNA double helix can lead to mutations.

Keywords: Base pairing; Density functional theory; Deprotonation; DNA duplication; Duplication rate; Guanine neutral radical; Nucleotides; Oxidative DNA damage; Radical lifetime