<br>DNA、RNA 和杂交双螺旋的温度依赖性弹性,Biophysical Journal

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DNA、RNA 和杂交双螺旋的温度依赖性弹性
Biophysical Journal ( IF 3.2 ) Pub Date : 2024-02-02 , DOI: 10.1016/j.bpj.2024.01.032
Hana Dohnalová ₁ , Eva Matoušková ₁ , Filip Lankaš ₁

Affiliation

DNA、RNA 和 DNA-RNA 杂交形式的核酸双螺旋在生物学中起着重要作用，是人工纳米结构的主要组成部分，但它们的性质如何取决于温度仍然知之甚少。在这里，我们报告了 DNA、RNA 和杂交双链体在 7°C 和 47°C 之间的动态弯曲持久性长度、扭曲刚度、拉伸模量和扭曲-拉伸耦合的热依赖性。结果基于使用不同力场参数化的全原子分子动力学模拟。我们首先证明，不受约束的分子动力学可以在室温下重现实验上已知的双链体机械性质。除了实验已知的特征外，我们还推断了混合双工的扭曲刚度和扭曲-拉伸耦合。至于温度依赖性，我们发现温度升高会软化所有双链体的弯曲、扭曲和拉伸。拉伸模量的相对降低为 0.003–0.004/°C，尽管它们的拉伸刚度非常不同，但所有双链变体都相似，而 RNA 扭曲刚度降低 0.003/°C，并且其他弹性模量的值更小。扭拉伸联轴器几乎不受温度影响。拉伸刚度、弯曲刚度和扭曲刚度都包含一个重要的熵分量。讨论了我们的结果与 DNA 灵活性的两种状态模型的关系。我们的工作在微秒尺度上提供了与蛋白质结合初始阶段相关的核酸双链体的温度依赖性弹性。

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Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003–0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

更新日期：2024-02-02

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