Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 China.
J Phys Chem B. 2014 Jan 30;118(4):915-20. doi: 10.1021/jp409247d. Epub 2014 Jan 14.
Computational chemistry approach was applied to explore the nature of electron attachment to cytosine-rich DNA single strands. An oligomer dinucleoside phosphate deoxycytidylyl-3',5'-deoxycytidine (dCpdC) was selected as a model system for investigations by density functional theory. Electron distribution patterns for the radical anions of dCpdC in aqueous solution were explored. The excess electron may reside on the nucleobase at the 5' position (dC(•-)pdC) or at the 3' position (dCpdC(•-)). From comparison with electron attachment to the cytosine related DNA fragments, the electron affinity for the formation of the cytosine-centered radical anion in DNA is estimated to be around 2.2 eV. Electron attachment to cytosine sites in DNA single strands might cause perturbations of local structural characteristics. Visible absorption spectroscopy may be applied to validate computational results and determine experimentally the existence of the base-centered radical anion. The time-dependent DFT study shows the absorption around 550-600 nm for the cytosine-centered radical anions of DNA oligomers. This indicates that if such species are detected experimentally they would be characterized by a distinctive color.
计算化学方法被应用于探索电子与富含胞嘧啶的 DNA 单链结合的本质。选择二核苷酸磷酸脱氧胞苷-3',5'-脱氧胞苷（dCpdC）作为研究的模型体系，通过密度泛函理论进行研究。探索了在水溶液中 dCpdC 自由基阴离子的电子分布模式。多余的电子可能位于 5' 位的核碱基上（dC(•-)pdC）或 3' 位（dCpdC(•-)）。通过与胞嘧啶相关的 DNA 片段的电子亲和性比较，估计 DNA 中形成胞嘧啶中心自由基阴离子的电子亲合能约为 2.2eV。电子与 DNA 单链上胞嘧啶位点的结合可能会引起局部结构特征的扰动。可见吸收光谱可用于验证计算结果，并确定实验中碱基中心自由基阴离子的存在。时间相关的 DFT 研究表明，DNA 寡聚物中胞嘧啶中心自由基阴离子的吸收在 550-600nm 左右。这表明如果实验中检测到此类物质，它们将具有独特的颜色特征。
