Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules
Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules
复制标题
DOI：
10.1103/physrevlett.100.118301
复制
发表时间：
2008-03-21
影响因子：
8.6
通讯作者：
van der Maarel, Johan R. C.
中科院分区：
文献类型：
--
作者：
Dai, Liang;Mu, Yuguang;van der Maarel, Johan R. C.
所有使用明确水的原子分子动力学模拟都是为了研究在多价抗衡离子腐胺 (2+)、亚精胺 (3+)、精胺 (4+) 和六胺钴 (3+) 存在下两个平行双链 DNA 分子之间的相互作用。 DNA 间相互作用势是通过伞式采样技术获得的。吸引力通过离子桥的形成而合理化，即同时结合到两个相对的 DNA 分子的多价离子。离子桥的寿命很短，只有几纳秒。
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.