The molecular mechanism of specific interactions between double stranded DNA molecules has been investigated for many years. Problems remain in how confinement, ions, and condensing agents change the interactions. We consider how the orientational alignment of DNAs contributes to the interactions via free energy simulations. Here we report on the effective interactions between two parallel DNA double helices in 150-mM NaCl solution using all atom models. We calculate the potential of mean force (PMF) of DNA-DNA interactions as a function of two coordinates, interhelical separation of parallel double helices and relative rotation of a DNA molecule with respect to the other about the helical axis. We generate the two-dimensional PMF to better understand the effective interactions when a DNA molecule is in juxtaposition with another. The analysis of the ion and solvent distributions around the DNA and particularly in the interface region shows that certain alignments of the DNA pair enhance the interactions. At local free energy minima in distance and alignment, water molecules and $\mathrm{N}{\mathrm{a}}^{+}$ ions form a hydrogen bonded network with the phosphates from each DNA. This network contributes an attractive energy component to the DNA-DNA interactions. Our results provide a molecular mechanism whereby local DNA-DNA interactions, depending on the helical orientation, give a potential mechanism for stabilizing pairing of much larger lengths of homologous DNA that have been seen experimentally. The study suggests an atomically detailed local picture of relevance to certain aspects of DNA condensation or aggregation.

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相同的DNA双螺旋之间的相互作用

已经研究了双链DNA分子之间特异性相互作用的分子机制。约束，离子和凝聚剂如何改变相互作用仍然存在问题。我们考虑DNA的定向比对如何通过自由能模拟促进相互作用。在这里，我们报告使用所有原子模型在150mM NaCl溶液中两个平行DNA双螺旋之间的有效相互作用。我们计算作为两个坐标，平行双螺旋的螺旋间距和一个DNA分子相对于另一个绕螺旋轴的相对旋转的函数，DNA-DNA相互作用的平均力（PMF）的潜力。我们生成二维PMF，以更好地理解当一个DNA分子与另一个并列时的有效相互作用。对DNA周围（尤其是在界面区域中）离子和溶剂分布的分析表明，DNA对的某些比对可增强相互作用。在距离和方向的局部自由能极小值处，水分子和$\mathrm{ñ}{\mathrm{一种}}^{+}$离子与每个DNA的磷酸盐形成氢键网络。该网络为DNA-DNA相互作用贡献了有吸引力的能量成分。我们的结果提供了一种分子机制，其中局部DNA-DNA相互作用（取决于螺旋方向）提供了一种稳定机制的潜在机制，该机制可以通过实验观察到更长的同源DNA。该研究提出了与DNA缩合或聚集的某些方面相关的原子详细局部图片。