Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
J Phys Chem B. 2013 Jun 20;117(24):7221-7. doi: 10.1021/jp4010955. Epub 2013 Jun 7.
One of the fundamental problems in nucleic acids biophysics is to predict the different forces that stabilize nucleic acid tertiary folds. Here we provide a quantitative estimation and analysis for the forces between DNA helices in an ionic solution. Using the generalized Born model and the improved atomistic tightly binding ions model, we evaluate ion correlation and solvent polarization effects in interhelix interactions. The results suggest that hydration, Coulomb correlation and ion entropy act together to cause the repulsion and attraction between nucleic acid helices in Mg(2+) and Mn(2+) solutions, respectively. The theoretical predictions are consistent with experimental findings. Detailed analysis further suggests that solvent polarization and ion correlation both are crucial for the interhelix interactions. The theory presented here may provide a useful framework for systematic and quantitative predictions of the forces in nucleic acids folding.
核酸生物物理学中的一个基本问题是预测稳定核酸三级折叠的不同力。在这里，我们对离子溶液中 DNA 螺旋之间的力进行了定量估计和分析。我们使用广义 Born 模型和改进的原子紧束缚离子模型，评估了螺旋间相互作用中的离子相关和溶剂极化效应。结果表明，水合作用、库仑相关和离子熵共同作用，分别导致了 Mg(2+)和 Mn(2+)溶液中核酸螺旋之间的排斥和吸引。理论预测与实验结果一致。详细分析进一步表明，溶剂极化和离子相关对于螺旋间相互作用都是至关重要的。本文提出的理论可能为系统地、定量地预测核酸折叠中的力提供了一个有用的框架。
