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. 2012 Jun 1;17(6):6705-15.
doi: 10.3390/molecules17066705.

Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine

Masayo Suzuki  1 , Katsuhito Kino, Masayuki Morikawa, Takanobu Kobayashi, Rie Komori, Hiroshi Miyazawa
Affiliations

Calculation of the stabilization energies of oxidatively damaged guanine base pairs with guanine

Masayo Suzuki et al. Molecules. .

Abstract

DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

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Figures

Scheme 1
Scheme 1
Oxidation products of guanine.
Figure 1
Figure 1
The Ia:G base pairs. (a) The proposed Ia:G base pair. (b) The proposed Ia:G base pairs and the associated hydrogen bonds. This numbering is the same as used in reference 13. (c) The geometries of Ia1:G-Ia8:G optimized by ab initio calculation. The stabilization energies are shown in 1.
Figure 2
Figure 2
The Gh:G base pairs. (a) The proposed Gh:G base pair. (b) The geometries of Gh1:G-Gh16:G optimized by ab initio calculation. The stabilization energies are shown in 1.
Figure 3
Figure 3
The Sp:G base pairs. (a) The proposed Sp:G base pair. (b) The geometries of Sp1:G and Sp2:G optimized by ab initio calculation. The stabilization energies are shown in 1.
Figure 4
Figure 4
The Oz:G base pair. (a) The proposed Oz:G base pair; (b) The geometries of Oz:G optimized by ab initio calculation. The stabilization energies are shown in 1.
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