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化学学报
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化学学报 ›› 2008, Vol. 66 ›› Issue (24): 2693-2699. 上一篇    下一篇

研究论文

溴化乙锭对B-DNA碱基对特异性识别的分子模拟研究

王志群a,b 张志强a 余江河a 倪坤仪a 何 华*,a,b

  

  1. (a中国药科大学分析化学教研室 南京 210009)
    (b中国药科大学药物质量与安全预警教育部重点实验室 南京 210009)

  • 投稿日期:2007-12-13 修回日期:2008-07-25 发布日期:2008-12-28
  • 通讯作者: 何华

Specificity Recognition of Base Pairs of B-DNA by Ethidium Bromide via Molecular Simulation

WANG, Zhi-Qun a,b ZHANG, Zhi-Qiang a YU, Jiang-He a NI, Kun-Yi a HE, Hua *, a,b   

  1. (a Division of Analytical Chemistry, China Pharmaceutical University, Nanjing 210009)
    (b Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009)
  • Received:2007-12-13 Revised:2008-07-25 Published:2008-12-28
  • Contact: HE, Hua

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被引次数

18 | 5

溴化乙锭是一种常用的DNA荧光探针, 其作用机制是通过插入作用与DNA分子形成稳定的复合物. 分子模拟显示, 溴化乙锭插入碱基对过程中有大小沟选择性, 对结合能的统计分析发现, 溴化乙锭分子更倾向从小沟方向插入到DNA分子中. 由溴化乙锭从小沟方向插入不同碱基对的结合能考察发现, 溴化乙锭对DNA碱基对有特异性识别, 并且与CA碱基对结合能最强. 对溴化乙锭插入DNA分子的驱动力和序列特异性识别的作用力分析, 揭示溴化乙锭插入DNA分子的驱动力和碱基对的特异性识别均以静电作用为主.

关键词: 溴化乙锭, 特异性识别, 计算机模拟, DNA, 碱基对

Ethidium bromide (EB) is commonly used as a fluorescent probe of B-DNA. The mechanism is the intercalation of EB into DNA base pairs to form a stable complex. It was found that the intercalation of EB had sequence specificity for B-DNA based on molecular simulation. Statistical analysis shows that EB prefers to intercalate into DNA from the minor groove, rather than from the major one. Comparing the binding energy of EB with different base pairs, it was found that EB had special recognition among base pairs with the maximum binding energy with CA. Through analyzing the driving energy of intercalation and the force of sequence special recognition, it can be concluded that both the intercalation and special recognition are mainly through electrostatical interaction.

Key words: ethidium bromide, specificity recognition, computer simulation, DNA, base pair