Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland.
Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA.
J Biomol Struct Dyn. 2023 Jul;41(10):4383-4397. doi: 10.1080/07391102.2022.2067239. Epub 2022 Apr 25.
The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM] cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM] cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage.Communicated by Ramaswamy H. Sarma.
DNA 的结构稳定性很重要，因为它具有生物活性。由于 DNA 固有的化学性质，其在水溶液中并不稳定，因此，在生物科学中，DNA 在环境条件下的长期储存非常重要。与有机溶剂和水相比，离子液体 (ILs) 由于其相当多的特性，是一种很有前途的替代品，可以用作新的试剂，以提高 DNA 的稳定性，使其能够长时间储存。在本文中，应用分子动力学 (MD) 模拟和量子化学计算研究了氨基酸离子液体 ([BMIM][Ala]、[BMIM][Gly]、[BMIM][Val]、[BMIM][Pro] 和 [BMIM][Leu]) 对小牛胸腺 DNA 动力学行为和结构稳定性的影响。根据获得的 MD 结果，ILs 进入 DNA 的溶剂化壳，并将水分子从 DNA 表面推开。结构分析表明，[BMIM]阳离子可以进入 DNA 小沟，而不会破坏 DNA 的双螺旋结构。ILs 由于与 DNA 结构的强静电和范德华 (vdW) 相互作用，有助于双螺旋结构的稳定性。量子化学计算表明，[BMIM]阳离子与 DNA 结构之间的相互作用具有静电性质。此外，与 AATT 碱基对相比，这种阳离子与 DNA 中 CGCG 区域形成更稳定的配合物。总的来说，这项研究的结果可以为在长期储存过程中使用 ILs 来维持 DNA 稳定性提供新的见解。
