Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain.
Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain.
J Chem Inf Model. 2023 Aug 28;63(16):5259-5271. doi: 10.1021/acs.jcim.3c00741. Epub 2023 Aug 14.
Sequence-dependent properties of the DNA duplex have been accurately described using extensive molecular dynamics simulations. The RNA duplex meanwhile─which is typically represented as a sequence-averaged rigid rod─does not benefit from having equivalent molecular dynamics simulations. In this paper, we present a massive simulation effort using a set of ABC-optimized duplexes from which we derived tetramer-resolution properties of the RNA duplex and a simple mesoscopic model that can represent elastic properties of long RNA duplexes. Despite the extreme chemical similarity between DNA and RNA, the local and global elastic properties of the duplexes are very different. DNA duplexes show a complex and nonelastic pattern of flexibility, for instance, while RNA duplexes behave as an elastic system whose deformations can be represented by simple harmonic potentials. In RNA duplexes (RNA), not only are intra- and interbase pair parameters (equilibrium and mechanical) different from those in the equivalent DNA duplex sequences (DNA) but the correlations between movements also differ. Simple statements on the relative flexibility or stability of both polymers are meaningless and should be substituted by a more detailed description depending on the sequence and the type of deformation considered.
使用广泛的分子动力学模拟可以准确描述 DNA 双链体的序列依赖性性质。然而，RNA 双链体——通常表示为序列平均刚性棒——无法从等效的分子动力学模拟中受益。在本文中，我们进行了大量的模拟工作，使用了一组经过 ABC 优化的双链体，从中我们得出了 RNA 双链体的四聚体分辨率性质和一个简单的介观模型，该模型可以表示长 RNA 双链体的弹性性质。尽管 DNA 和 RNA 在化学上非常相似，但双链体的局部和整体弹性性质却大不相同。例如，DNA 双链体表现出复杂而非弹性的灵活性模式，而 RNA 双链体则表现为弹性系统，其变形可以用简单的谐波势来表示。在 RNA 双链体（RNA）中，不仅碱基对参数（平衡和力学）与等效的 DNA 双链体序列（DNA）不同，而且运动之间的相关性也不同。简单地陈述两种聚合物的相对灵活性或稳定性是没有意义的，应该根据序列和考虑的变形类型用更详细的描述来代替。
