Sundaresan Neethu, Suresh Cherumuttathu H
Chemical Sciences and Technology Division and Computational Modeling and Simulation Section, Regional Research Laboratory (Council of Scientific and Industrial Research), Trivandrum 695019, India.
J Chem Theory Comput. 2007 May;3(3):1172-82. doi: 10.1021/ct600245w.
A three-layer ONIOM approach was used to study the interactions of hydrated alkali metal ions such as Li(+), Na(+), and K(+) with a DNA fragment containing two phosphate groups, three sugar units, and a G••C base pair modeled in the anion and dianion states. Among the three metal-binding combinations studied herein (outer-sphere, inner-sphere monodentate, and inner-sphere bidentate), the outer-sphere binding mode showed the highest binding energy (BE) for hydrated Li(+) ions (103.1 kcal/mol) while the hydrated Na(+) and K(+) ions preferred the inner-sphere monodentate binding modes to the phosphate group of the anionic DNA fragment (BE = 87.9 and 98.2 kcal/mol for Na(+) and K(+), respectively). These data on the binding mechanisms of Li(+), Na(+), and K(+) ions and the higher binding affinity of Li(+) ions compared to Na(+) and K(+) ions in the anion model system of DNA are in good agreement with the previous experimental findings. On the other hand, in the dianion state, Li(+) preferred inner-sphere monodentate, whereas Na(+) and K(+) ions preferred the outer-sphere structures. The neutral anion model ion revealed a more realistic picture of DNA-alkali metal ion interactions compared to the non-neutral dianion model systems.
采用三层ONIOM方法研究了水合碱金属离子（如Li(+)、Na(+)和K(+)）与一个包含两个磷酸基团、三个糖单元以及一个处于阴离子和二价阴离子状态的G••C碱基对的DNA片段之间的相互作用。在本文研究的三种金属结合组合（外层球、内层球单齿和内层球双齿）中，外层球结合模式对水合Li(+)离子显示出最高的结合能（BE）（103.1 kcal/mol），而水合Na(+)和K(+)离子更倾向于与阴离子DNA片段的磷酸基团形成内层球单齿结合模式（Na(+)和K(+)的BE分别为87.9和98.2 kcal/mol）。这些关于Li(+)、Na(+)和K(+)离子结合机制的数据以及在DNA阴离子模型系统中Li(+)离子相对于Na(+)和K(+)离子具有更高的结合亲和力，与先前的实验结果高度一致。另一方面，在二价阴离子状态下，Li(+)更倾向于内层球单齿，而Na(+)和K(+)离子更倾向于外层球结构。与非中性二价阴离子模型系统相比，中性阴离子模型离子揭示了更真实的DNA - 碱金属离子相互作用情况。
