Jumbri K, Abdul Rahman M B, Abdulmalek E, Ahmad H, Micaelo N M
Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
Phys Chem Chem Phys. 2014 Jul 21;16(27):14036-46. doi: 10.1039/c4cp01159g. Epub 2014 Jun 5.
Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL-DNA could be used as a basis for future development of specific ILs for nucleic acid technology.
采用分子动力学模拟和生物物理分析来揭示离子液体（ILs）对DNA结构特性的影响。计算和实验证据均表明，DNA在离子液体中保持其天然的B构象。模拟数据表明，DNA磷酸基团周围的水合壳是该离子介质中DNA稳定的主要标准。更强的水合壳会降低离子液体阳离子与DNA磷酸基团的结合能力，从而使DNA不稳定。模拟结果还表明，在高达373.15 K的不同温度下，当DNA被离子液体溶剂化时，其结构保持双链构象。该结果进一步表明，DNA在高温下的热稳定性与溶剂热力学有关，尤其是水的熵和焓。所有分子模拟结果均与实验结果一致。对离子液体 - DNA特性的理解可作为未来开发用于核酸技术的特定离子液体的基础。
