溴化乙锭对B-DNA碱基对特异性识别的分子模拟研究

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

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.

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.