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2007 | 5 | 1 | 49-61

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Structural analysis of base mispairing in DNA containing oxidative guanine lesion


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Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.










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1 - 3 - 2007
1 - 3 - 2007


  • Division of Radiological Protection and Biology, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo, 162-8640, Japan
  • Japan Atomic Energy Agency, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan
  • Research Organization for Information Science and Technology, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan
  • Japan Atomic Energy Agency, Shirakata, Shirane 2-4, Tokai-mura, Ibaraki, 319-1195, Japan


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