Joint Institute of IRB/BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona, Spain.
Biophys J. 2010 Sep 22;99(6):1876-85. doi: 10.1016/j.bpj.2010.06.061.
The structure and flexibility of the RNA duplex has been studied using extended molecular dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many copies of the 10 unique dinucleotide steps in different sequence environments. Simulations were performed using the two most popular force fields for nucleic acids simulations (AMBER and CHARMM) in their latest versions, trying to arrive to a consensus picture of the RNA flexibility. Contrary to what was found for DNA duplex (DNA(2)), no clear convergence is found for the RNA duplex (RNA(2)), but one of the force field seems to agree better with experimental data. MD simulations performed with this force field were used to fully characterize, for the first time to our knowledge, the sequence-dependent elastic properties of RNA duplexes at different levels of resolutions. The flexibility pattern of RNA(2) shows similarities with DNA(2), but also surprising differences, which help us to understand the different biological functions of both molecules. A full mesoscopic model of RNA duplex at different resolution levels is derived to be used for genome-wide description of the flexibility of double-helical fragments of RNA.
使用针对不同序列环境中包含许多独特二核苷酸步骤的 18 个核苷酸设计的四个不同的 18 个核苷酸寡核苷酸，通过扩展分子动力学模拟研究了 RNA 双链体的结构和柔韧性。使用最新版本的两种最流行的核酸模拟力场（AMBER 和 CHARMM）进行了模拟，试图达成 RNA 柔韧性的共识。与 DNA 双链体（DNA(2)）的发现相反，对于 RNA 双链体（RNA(2)）没有发现明确的收敛性，但其中一种力场似乎与实验数据更吻合。使用该力场进行的 MD 模拟首次全面表征了在不同分辨率水平下 RNA 双链体的序列依赖性弹性特性。RNA(2)的柔韧性模式与 DNA(2)相似，但也存在令人惊讶的差异，这有助于我们理解这两种分子的不同生物学功能。为了在全基因组范围内描述 RNA 双链体片段的柔韧性，还衍生出了不同分辨率水平的 RNA 双链体的全介观模型。
