Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex

作者：Zhang, Zhong-Liang; Wu, Yuan-Yan; Xi, Kun; Sang, Jian-Ping^*; Tan, Zhi-Jie^*

来源：Biophysical Journal, 2017, 113(3): 517-528.

DOI：10.1016/j.bpj.2017.06.021

• MOLECULAR-DYNAMICS SIMULATIONS
• COUNTERION-INDUCED CONDENSATION
• HELIX-HELIX INTERACTIONS
• DOUBLE-STRANDED DNA
• POLYELECTROLYTE SOLUTIONS
• CHARGED NANOPARTICLES
• INTERMOLECULAR FORCES
• NUCLEIC-ACIDS
• MEAN FORCE
• RNA

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.

• 出版日期2017-8-8
• 单位武汉大学; 扬州大学