Binding of Cationic Conjugated Polymers to DNA: Atomistic Simulations of Adducts Involving the Dickerson鈥檚 Dodecamer

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• 作者：Julien Preat ; David Zanuy ; Eric A. Perpe虁te ; Carlos Alema虂n
• 刊名：Biomacromolecules
• 出版年：2011
• 出版时间：April 11, 2011
• 年：2011
• 卷：12
• 期：4
• 页码：1298-1304
• 全文大小：924K
• 年卷期：v.12,no.4(April 11, 2011)
• ISSN：1526-4602

文摘

We here describe the investigation at the atomistic level of the structure, stability, and dynamics of several complexes resulting from the interaction of oxidized poly(3,4-ethylenedioxythiophene) with the well-known Dickerson鈥檚 dodecamer sequence. Four specific arrangements have been selected as referential structures for molecular dynamics simulations, and the resulting independent trajectories tend to converge in two distinguishable models with the strongest interactions. The first one presents a coiled DNA strand enveloping the oligomer chain, whereas in the second model, the conducting polymer chain and the disorganized DNA strand are facing side-by-side. Analysis of the intermolecular interactions indicates that the electrostatic interactions involving the negatively charged DNA phosphates and the positively charged units of the oligomer are much more frequent in the first model. In addition, aside from these electrostatic interactions, specific O路路路H and S路路路H hydrogen bonds, 蟺鈭捪€ stacking, and N鈭扝路路路蟺 interactions have been detected. Among all of these four specific interactions, we show that the 蟺鈭捪€ stacking is the most abundant and shows the best stability, whereas O路路路H hydrogen bonds are also frequent with long lifetimes. At the end, we have to underline that these specific interactions are predominant for the thymine and the guanine, which is in perfect agreement with previous experimental observations.