多价离子介导的核酸螺旋-螺旋相互作用：RNA与DNA
Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA
摘要：
离子介导的相互作用对核酸的结构和稳定性至关重要。最近的实验表明，多价离子诱导的双链RNA和DNA的聚集可能强烈依赖于螺旋的拓扑性质，而在原子水平上的离子介导的相关相互作用仍然缺乏理解。本文采用原子分子动力学模拟直接计算了六氨合钴离子（Co-Hex）溶液中双链RNA和双链DNA之间的平均力势（PMF）。计算结果表明，当[Co-Hex]较低时，B-DNA之间和A-RNA之间的PMF都是（强）排斥的，而当[Co-Hex]较高时，B-DNA之间的PMF是强吸引的，而A-RNA之间和A-DNA之间的PMF仍然是（弱）排斥的。微观分析表明，对于A型螺旋，Co-Hex将成为深大沟的内结合，从而不能在相邻螺旋之间形成明显的离子桥;而对于没有深大沟的B型螺旋，Co-Hex将表现出外结合，从而强有力地桥接相邻螺旋。此外，我们进一步的计算表明，A-RNA之间的PMF可能会变得很强的吸引力，无论是在很高的[Co-Hex]或当深大沟底部固定有一层水。
英文摘要：
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Cobalt Hexammine ion (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive.However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become internal binding into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit external binding to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.
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