Hydrophobic Organic Linkers in the Self-Assembly of Small Molecule-DNA Hybrid Dimers: A Computational鈥揈xperimental Study of the Role of Linkage Direction in Product Distributions and Stabilities

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• 作者：Ilyas Yildirim ; Ibrahim Eryazici ; SonBinh T. Nguyen ; George C. Schatz
• 刊名：Journal of Physical Chemistry B
• 出版年：2014
• 出版时间：March 6, 2014
• 年：2014
• 卷：118
• 期：9
• 页码：2366-2376
• 全文大小：544K
• 年卷期：v.118,no.9(March 6, 2014)
• ISSN：1520-5207

文摘

Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3鈥?ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5鈥?ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.