School of Physics and Technology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
J Chem Phys. 2024 Aug 21;161(7). doi: 10.1063/5.0211869.
The elasticities of double-stranded (ds) DNA and RNA, which are critical to their biological functions and applications in materials science, can be significantly modulated by solution conditions such as ions and temperature. However, there is still a lack of a comprehensive understanding of the role of solvents in the elasticities of dsRNA and dsDNA in a comparative way. In this work, we explored the effect of ethanol solvent on the elasticities of dsRNA and dsDNA by magnetic tweezers and all-atom molecular dynamics simulations. We found that the bending persistence lengths and contour lengths of dsRNA and dsDNA decrease monotonically with the increase in ethanol concentration. Furthermore, the addition of ethanol weakens the positive twist-stretch coupling of dsRNA, while promotes the negative twist-stretch coupling of dsDNA. Counter-intuitively, the lower dielectric environment of ethanol causes a significant re-distribution of counterions and enhanced ion neutralization, which overwhelms the enhanced repulsion along dsRNA/dsDNA, ultimately leading to the softening in bending for dsRNA and dsDNA. Moreover, for dsRNA, ethanol causes slight ion-clamping across the major groove, which weakens the major groove-mediated twist-stretch coupling, while for dsDNA, ethanol promotes the stretch-radius correlation due to enhanced ion binding and consequently enhances the helical radius-mediated twist-stretch coupling.
双链 (ds) DNA 和 RNA 的弹性对于它们的生物学功能和在材料科学中的应用至关重要，溶液条件（如离子和温度）可以显著调节其弹性。然而，对于溶剂在双链 RNA 和 dsDNA 弹性中的作用，我们仍然缺乏全面的了解，尤其是缺乏比较性的理解。在这项工作中，我们通过磁镊和全原子分子动力学模拟研究了乙醇溶剂对 dsRNA 和 dsDNA 弹性的影响。我们发现，dsRNA 和 dsDNA 的弯曲持久长度和轮廓长度随乙醇浓度的增加而单调下降。此外，乙醇的添加削弱了 dsRNA 的正扭转拉伸耦合，而促进了 dsDNA 的负扭转拉伸耦合。出人意料的是，乙醇的低介电环境导致反离子的重新分布和增强的离子中和，这超过了 dsRNA/dsDNA 上增强的排斥力，最终导致 dsRNA 和 dsDNA 的弯曲软化。此外，对于 dsRNA，乙醇在主沟内引起轻微的离子夹持，从而削弱了主沟介导的扭转拉伸耦合，而对于 dsDNA，由于离子结合增强，乙醇促进了拉伸半径相关性，从而增强了螺旋半径介导的扭转拉伸耦合。
