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Sequence-dependent mechanical properties of double-stranded RNA†
Nanoscale ( IF 5.8 ) Pub Date : 2019-11-04 , DOI: 10.1039/c9nr07516j Alberto Marin-Gonzalez 1, 2, 3, 4, 5 , J. G. Vilhena 5, 6, 7, 8, 9 , Fernando Moreno-Herrero 1, 2, 3, 4, 5 , Ruben Perez 5, 6, 7, 8, 10
Nanoscale ( IF 5.8 ) Pub Date : 2019-11-04 , DOI: 10.1039/c9nr07516j Alberto Marin-Gonzalez 1, 2, 3, 4, 5 , J. G. Vilhena 5, 6, 7, 8, 9 , Fernando Moreno-Herrero 1, 2, 3, 4, 5 , Ruben Perez 5, 6, 7, 8, 10
Affiliation
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The mechanical properties of double-stranded RNA (dsRNA) are involved in many of its biological functions and are relevant for future nanotechnology applications. DsRNA must tightly bend to fit inside viral capsids or deform upon the interaction with proteins that regulate gene silencing or the immune response against viral attacks. However, the question of how the nucleotide sequence affects the global mechanical properties of dsRNA has so far remained largely unexplored. Here, we have employed state-of-the-art atomistic molecular dynamics simulations to unveil the mechanical response of different RNA duplexes to an external force. Our results reveal that, similarly to dsDNA, the mechanical properties of dsRNA are highly sequence-dependent. However, we find that the nucleotide sequence affects in a strikingly different manner the stretching and twisting response of RNA and DNA duplexes under force. We find that the elastic response of dsRNA is dominated by the local high flexibility of pyrimidine-purine steps. Moreover, the flexibility of pyrimidine-purine steps is independent of the sequence context, and the global flexibility of the duplex reasonably scales with the number of this kind of base-pair dinucleotides. We conclude that disparities of the mechanical response of dinucleotides are responsible for the differences observed in the mechanical properties of RNA and DNA duplexes.
中文翻译：
双链RNA的序列依赖性机械性能†
双链RNA（dsRNA）的机械特性涉及其许多生物学功能，并且与未来的纳米技术应用相关。DsRNA必须紧紧弯曲以适合病毒衣壳内部，或者在与调节基因沉默或抵抗病毒攻击的免疫反应的蛋白质相互作用时发生变形。然而，迄今为止，关于核苷酸序列如何影响dsRNA的整体机械性质的问题仍未得到充分探讨。在这里，我们采用了最先进的技术原子分子动力学模拟，揭示了不同RNA双链体对外力的机械响应。我们的结果表明，与dsDNA相似，dsRNA的机械性能高度依赖序列。但是，我们发现核苷酸序列在力的作用下以显着不同的方式影响RNA和DNA双链体的拉伸和扭曲反应。我们发现，dsRNA的弹性反应主要由嘧啶-嘌呤步骤的局部高柔韧性决定。而且，嘧啶-嘌呤步骤的灵活性与序列背景无关，并且双链体的全局灵活性与这种碱基对二核苷酸的数目合理地成比例。
更新日期：2019-11-14
中文翻译：
双链RNA的序列依赖性机械性能†
双链RNA（dsRNA）的机械特性涉及其许多生物学功能，并且与未来的纳米技术应用相关。DsRNA必须紧紧弯曲以适合病毒衣壳内部，或者在与调节基因沉默或抵抗病毒攻击的免疫反应的蛋白质相互作用时发生变形。然而，迄今为止，关于核苷酸序列如何影响dsRNA的整体机械性质的问题仍未得到充分探讨。在这里，我们采用了最先进的技术原子分子动力学模拟，揭示了不同RNA双链体对外力的机械响应。我们的结果表明，与dsDNA相似，dsRNA的机械性能高度依赖序列。但是，我们发现核苷酸序列在力的作用下以显着不同的方式影响RNA和DNA双链体的拉伸和扭曲反应。我们发现，dsRNA的弹性反应主要由嘧啶-嘌呤步骤的局部高柔韧性决定。而且，嘧啶-嘌呤步骤的灵活性与序列背景无关，并且双链体的全局灵活性与这种碱基对二核苷酸的数目合理地成比例。
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