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首页> 外文期刊>Chemistry: A European journal >Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove
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Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

机译：在主要DNA槽中结合的合成超分子圆柱体周围的DNA缠绕模拟

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In this work we present the results of a molecular simulation study of the interaction between a tetracat-ionic bis iron(II)supramolecular cylinder,[Fe_2(C_(25)H_(20)N_4)_3]~(4+),and DNA.This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA.The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes.Three sets of multi-nanosecond simulations have been performed:one of the uncomplexed d(CCCCCTTTTTCC)-d(GGAAAAAGGGGG)dodecamer;one of this DNA complexed with the cylinder molecule;and one of this DNA complexed with a neutralised version of the cylinder.Coiling of the DNA was observed in the DNA-cylin-der simulations,giving insight into the molecular level nature of the supramo-lecular coiling observed experimentally.The cylinder charge was found not to be essential for the DNA coiling,which implies that the DNA response is moderated by the short range interactions that define the molecular shape.Cylinder charge did,however,affect the integrity of the DNA duplex,to the extent that,under some circumstances,the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.
机译：在这项工作中，我们提供了分子模拟研究的结果，该分子模拟研究了四阳离子双金属双铁（II）超分子圆柱体[Fe_2（C_（25_H_（20）N_4）_3]〜（4+）和DNA。该超分子圆柱体已显示出结合在DNA的主要沟中并引起DNA的剧烈卷曲。模拟设计旨在阐明导致圆柱体靶向主要沟并推动后续DNA构象的相互作用。进行了三组多纳秒模拟：未复合的d（CCCCCTTTTTCC）-d（GGAAAAAGGGGG）十二聚体;其中一种与圆柱分子复合的DNA;以及其中一种与中和形式的DNA复合的DNA。在DNA圆柱模拟中观察到了DNA的卷曲，从而洞察了实验观察到的超分子卷曲的分子水平性质。发现圆柱电荷对于DNA卷曲不是必需的，这表明DNA资源通过限定分子形状的短程相互作用来调节应答。但是，在某些情况下，圆柱电荷确实影响DNA双链体的完整性，以致在某些情况下，四阳离子圆柱在邻近位置的DNA碱基配对中引起缺陷。到圆柱结合位点。

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