引用本文:
马国正, 求亚芳, 南俊民, 肖信. DNA小沟结合二脒:水分子的识别作用[J]. 物理化学学报,
2008, 24(10): 1917-1921.
doi:
10.3866/PKU.WHXB20081031
Citation: MA Guo-Zheng, QIU Ya-Fang, NAN Jun-Min, XIAO Xin. DNA Minor Groove Binding by Diamidine:Water Molecule in Ligand Recognition[J]. Acta Physico-Chimica Sinica, 2008, 24(10): 1917-1921. doi: 10.3866/PKU.WHXB20081031
Citation: MA Guo-Zheng, QIU Ya-Fang, NAN Jun-Min, XIAO Xin. DNA Minor Groove Binding by Diamidine:Water Molecule in Ligand Recognition[J]. Acta Physico-Chimica Sinica, 2008, 24(10): 1917-1921. doi: 10.3866/PKU.WHXB20081031
DNA小沟结合二脒:水分子的识别作用
摘要:
采用分子动力学模拟了DB921-DNA复合物, 通过7 ns的模拟研究表明: DB921一端的氨基氮原子与一个水分子形成氢键, 同时, 水分子又与DNA的5位A碱基的氮原子形成一个氢键. 水分子在DB921与DNA小沟结合中起了桥连的作用, 使得直线型的芳香二脒化合物DB921通过水桥与DNA小沟结合, 水分子诱导DB921分子与DNA的小沟域构型相适应, 与DNA小沟域的AATTC碱基有较强的结合作用. 在分子水平上提供了DB921与双螺旋DNA相互作用的结构及复合物的动态变化情况, 指出水分子在DNA小沟结合二脒化合物中的识别作用, 为设计出更高生物活性的DNA小沟结合剂提供一定的理论依据.
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关键词:
- 小沟结合; 二脒; 水分子; 分子识别
English
DNA Minor Groove Binding by Diamidine:Water Molecule in Ligand Recognition
Abstract:
Molecular dynamics simulations were used to investigate the interaction of DB921 with the DNA oli nucleotide d[CGCGAATTCGCG]2. A 7 ns MD calculation was performed to study the DB921-DNA complex and the results indicated that DB921 was inserted in the minor groove of DNA, binding to the region of duplex AATTC bases. A water molecule forms bifurcated pair of H-bonds between the N atom of benzimidazole ring and N3 atom of the adenine 5 in the DB921-DNA complex. This water molecule performs a key bridging role which induces a more favorable curvature configuration and matches well the DNA minor groove topology. Molecular dynamics studies complemented the structural analysis and offered a clear picture of the water-bridge, providing the theoretical guidance for the design of biologically active minor groove agents.
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