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Molecules 2014, 19(8), 11030-11044; doi:10.3390/molecules190811030

Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine

Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1, Shido, Sanuki, Kagawa 769-2193, Japan
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Received: 27 May 2014 / Revised: 17 July 2014 / Accepted: 21 July 2014 / Published: 28 July 2014
(This article belongs to the Special Issue ECSOC-17)
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Abstract

DNA is constantly being oxidized, and oxidized DNA is prone to mutation; moreover, guanine is highly sensitive to several oxidative stressors. Several oxidatively damaged forms of guanine—including 2,2,4-triamino-5(2H)-oxazolone (Oz), iminoallantoin (Ia), and spiroiminodihydantoin (Sp)—can be paired with guanine, and cause G:C-C:G transversions. Previous findings indicate that guanine is incorporated more efficiently opposite Oz than opposite Ia or Sp, and that these differences in efficiency cannot be explained by differences in the stabilities of G:Oz, G:Ia, and G:Sp base pairs calculated ab initio. Here, to explain previous experimental result, we used a 3-base-pair model DNA duplex to calculate the difference in the stability and the distortion of DNA containing a G:Oz, G:Ia, or G:Sp base pair. We found that the stability of the structure containing 5ꞌ and 3ꞌ base pairs adjacent to G:Oz was more stable than that containing the respective base pairs adjacent to G:Ia or G:Sp. Moreover, the distortion of the structure in the DNA model duplex that contained a G:Oz was smaller than that containing a G:Ia or G:Sp. Therefore, our discussion can explain the previous results involving translesion synthesis past an oxidatively damaged guanine. View Full-Text
Keywords: oxidatively damaged guanine; base pair; distortion of DNA duplex; destabilization energy oxidatively damaged guanine; base pair; distortion of DNA duplex; destabilization energy
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MDPI and ACS Style

Suzuki, M.; Kino, K.; Morikawa, M.; Kobayashi, T.; Miyazawa, H. Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine. Molecules 2014, 19, 11030-11044.

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