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Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex
Biophysical Journal ( IF 3.2 ) Pub Date : 2017-08-01 , DOI: 10.1016/j.bpj.2017.06.021
Zhong-Liang Zhang 1 , Yuan-Yan Wu 2 , Kun Xi 1 , Jian-Ping Sang 1 , Zhi-Jie Tan 1
Affiliation  

Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.

中文翻译:

二价离子介导的 DNA-DNA 相互作用:三链体和双链体的比较研究

DNA 之间的离子介导相互作用对于 DNA 凝聚是必不可少的,一般认为单价和非特异性结合的二价阳离子不能诱导双链 (ds) DNA 的聚集。有趣的是,最近的实验发现,碱土金属离子如 Mg2+ 可以诱导三链 (ts) DNA 的聚集,尽管在微观层面对令人惊讶的发现仍然缺乏深入了解。在这项工作中,我们采用全原子动力学模拟来直接计算 Mg2+ 溶液中 tsDNA 之间、dsDNA 之间以及 tsDNA 和 dsDNA 之间的平均力 (PMF) 势。我们的计算表明,tsDNAs 之间的 PMF 显然具有吸引力,并且在 [Mg2+] 较高时变得更具吸引力,尽管 dsDNA 之间的 PMF 即使在高 [Mg2+] 下也不会变得明显有吸引力。我们的分析表明,对于 tsDNA 和 dsDNA,Mg2+ 在内部结合到凹槽中,并在外部与磷酸基团结合,而 Mg2+ 的外部结合对于 tsDNA 强得多。与 dsDNA 相比,tsDNA 的 Mg2+ 的这种更强的外部结合有利于螺旋之间更明显的离子桥接。此外,我们的分析表明,桥接离子作为外部结合离子的特殊部分,与 DNA 之间的离子介导的吸引力紧密且正耦合。与 dsDNA 相比,tsDNA 的 Mg2+ 的这种更强的外部结合有利于螺旋之间更明显的离子桥接。此外,我们的分析表明,桥接离子作为外部结合离子的特殊部分,与 DNA 之间的离子介导的吸引力紧密且正耦合。与 dsDNA 相比,tsDNA 的 Mg2+ 的这种更强的外部结合有利于螺旋之间更明显的离子桥接。此外,我们的分析表明,桥接离子作为外部结合离子的特殊部分,与 DNA 之间的离子介导的吸引力紧密且正耦合。
更新日期:2017-08-01
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