State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China.
Nanoscale. 2019 Jan 23;11(4):1827-1836. doi: 10.1039/c8nr06203j.
A better understanding of interactions between metal-nanomaterial surfaces and biomolecules such as DNAs is critical for their biomedical applications. Here we investigated double-stranded DNA (dsDNA) adhering to palladium (Pd) nanosheets with two different exposed facets, {100} and {111}, using a combined computational and experimental approach. Different dsDNA binding modes on the two surfaces were observed, with a surprising "upright" conformation on Pd(100) and a "flat" conformation on Pd(111). Molecular dynamics simulations showed a stronger binding of the dsDNA on Pd(111) than Pd(100), which resulted in significant conformational changes and hydrogen bond breakage in the dsDNA on Pd(111). Further analyses revealed that the different binding strengths were caused by the number and arrangement of water molecules in the first solvation shell (FSS) of the two Pd surfaces. The water hydrogen bond network in the FSS of Pd(100) is compact and resists the embedding of dsDNA, while it is less compact on Pd(111), which allows penetration of dsDNA and its direct contact with Pd(111) surface atoms, thereby exhibiting stronger binding. Further free energy calculations with umbrella sampling supported these observations. Finally, these computational predictions on the adsorption capacity of dsDNA on Pd surfaces were confirmed by gel electrophoresis experiments.
更好地理解金属纳米材料表面与生物分子（如 DNA）之间的相互作用对于它们的生物医学应用至关重要。在这里，我们采用计算与实验相结合的方法研究了具有两种不同暴露晶面（{100}和{111}）的钯纳米片上吸附的双链 DNA（dsDNA）。在两种表面上观察到不同的 dsDNA 结合模式，在 Pd(100)上呈现出令人惊讶的“直立”构象，而在 Pd(111)上呈现出“平面”构象。分子动力学模拟表明，dsDNA 在 Pd(111)上的结合比在 Pd(100)上更强，这导致 dsDNA 发生显著的构象变化和氢键断裂。进一步的分析表明，不同的结合强度是由两种 Pd 表面的第一溶剂化壳（FSS）中水分子的数量和排列引起的。Pd(100)的 FSS 中的水分子氢键网络紧凑，阻碍 dsDNA 的嵌入，而在 Pd(111)上则不那么紧凑，这允许 dsDNA 的渗透及其与 Pd(111)表面原子的直接接触，从而表现出更强的结合。进一步使用伞状采样的自由能计算支持了这些观察结果。最后，通过凝胶电泳实验证实了这些关于 dsDNA 在 Pd 表面吸附能力的计算预测。
