Chen Chuanying, Pettitt B Montgomery
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
Life (Basel). 2022 May 7;12(5):699. doi: 10.3390/life12050699.
A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is elucidated by studying the energetic properties of Na ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches.
深入了解离子介导的双链DNA相互作用的物理机制对于诸如DNA包装和同源配对等生物学功能至关重要。我们报告了在0.15 M NaCl溶液中，两条平行且相同的双链DNA之间的平均力势（PMF）或有效溶剂介导的相互作用随螺旋间距离的变化情况。在此，我们通过比较刚性模型和柔性模型之间的PMF，研究双链DNA的柔韧性对有效相互作用的影响。通过研究钠离子的能量特性以及双链DNA周围离子的波动情况，阐明了双链DNA对柔韧性在其缔合过程中的作用。双链DNA柔韧性的引入使范德华接触壁变软，并在双链DNA周围引发更多反离子波动。此外，柔韧性促进了钠离子的动力学，影响其分布。这些结果量化了双链DNA柔韧性对吸引力的影响程度，并进一步强调了非连续溶剂化方法的重要性。
