Molecular dynamics studies of ion distributions for DNA duplexes and DNA clusters: Salt effects and connection to DNA melting
Molecular dynamics studies of ion distributions for DNA duplexes and DNA clusters: Salt effects and connection to DNA melting
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DOI：
10.1021/jp0556815
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发表时间：
2006-02-16
影响因子：
3.3
通讯作者：
Schatz, GC
中科院分区：
文献类型：
--
作者：
Long, H;Kudlay, A;Schatz, GC
我们提出了广泛的分子动力学模拟的离子分布的DNA双链体和DNA簇使用琥珀力场与隐式水。在模拟结果的基础上，确定了在0.2-1.0 mol/L的范围内不同盐（NaCl）浓度下，离子在分离的DNA双链体和DNA双链体簇周围的分布和离子的静电能。利用静电能量分布，我们确定了一个局部的净电荷分数φ，这是随着盐浓度的增加而增加。对于含有两个DNA双链体（DNA对）或四个DNA双链体的DNA簇，phi随着双链体之间的距离减小而增大。结合这一结果与实验结果的DNA解链温度对散装盐浓度的依赖性，我们得出结论，对于一对DNA双链体的解链温度增加5 - 10 K的轴间分离的25 - 40埃。对于四个DNA双链体的簇，应该发生甚至更大的解链温度增加。我们认为，这种熔融温度增加密集的DNA簇是负责在DNA连接的纳米颗粒聚集体和DNA连接的聚合物聚集体的合作熔融机制。
We present extensive molecular dynamics simulations of the ion distributions for DNA duplexes and DNA clusters using the Amber force field with implicit water. The distribution of ions and the electrostatic energy of ions around an isolated DNA duplex and clusters of DNA duplexes in different salt (NaCl) concentrations over the range 0.2-1.0 mol/L are determined on the basis of the simulation results. Using the electrostatic energy profile, we determine a local net charge fraction phi, which is found to increase with increasing of salt concentration. For DNA clusters containing two DNA duplexes (DNA pair) or four DNA duplexes, phi increases as the distance between the duplexes decreases. Combining this result with experimental results for the dependence of the DNA melting temperature on bulk salt concentration, we conclude that for a pair of DNA duplexes the melting temperature increases by 5 - 10 K for interaxis separations of 25 - 40 angstrom. For a cluster of four DNA duplexes, an even larger melting temperature increase should occur. We argue that this melting temperature increase in dense DNA clusters is responsible for the cooperative melting mechanism in DNA-linked nanoparticle aggregates and DNA-linked polymer aggregates.