Toward a Consensus View of Duplex RNA Flexibility
Toward a Consensus View of Duplex RNA Flexibility
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DOI：
10.1016/j.bpj.2010.06.061
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发表时间：
2010-09-22
影响因子：
3.4
通讯作者：
Orozco, Modesto
中科院分区：
文献类型：
--
作者：
Faustino, Ignacio;Perez, Alberto;Orozco, Modesto
利用扩展的分子动力学模拟研究了RNA双链的结构和灵活性，模拟了四种不同的18聚寡核苷酸，这些寡核苷酸被设计成在不同的序列环境中包含10个独特的二核苷酸步骤的许多拷贝。使用最新版本的两种最流行的核酸模拟力场（AMBER和CHARMM）进行模拟，试图对RNA灵活性达成共识。与DNA双工（DNA(2)）的发现相反，RNA双工（RNA(2)）没有发现明显的收敛性，但其中一个力场似乎与实验数据更吻合。用该力场进行的MD模拟被用来全面表征，据我们所知，这是第一次，RNA双链在不同分辨率下的序列依赖弹性特性。RNA(2)的柔韧性模式显示出与DNA(2)的相似之处，但也有惊人的差异，这有助于我们理解这两种分子不同的生物学功能。一个完整的介观模型的RNA双工在不同的分辨率水平推导用于全基因组范围内的RNA的双螺旋片段的灵活性描述。
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.