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Conformational Changes of DNA Induced by trans-Azobenzene Derivative via Non-Covalent Interactions

Abstract

In biological environments and in aqueous solution DNA generally adopts the canonical B conformation. Recently, an azobenzene photoswitch containing a polyamine chain with three positive charges was shown to induce a reversible conformational transition between A and B forms of DNA, the transition being triggered by trans-cis isomerization of the photoswitch upon non-covalent intercalation. It was proposed that, in its trans conformation, the azobenzene stabilizes the A form of DNA. The structural details and the mechanism upon which trans-azobenzene induces B-to-A DNA transition remain, however, unclear. In the present contribution, two possible intercalating modes of trans-azobenzene e. g., from the minor groove and from the major groove, were investigated with all-atom molecular-dynamics simulations. Intercalation from the major groove is found to be the most probable binding mode due to favorable electrostatic and π-π stacking interactions. The free-energy profile associated to the B-to-A conformational transition reveals that intercalation from the major groove leads to a conformational change of DNA, showing a slight tendency to interconvert from B- to A-DNA, in agreement with the CD spectrum obtained from the experiment. However, the presence of only one interacting azobenzene is not sufficient to lead to a global conformational change to A-DNA. The present results are expected to serve in the design of DNA switches, which can induce reversible DNA conformational changes.

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Publication details

The article was received on 16 Jun 2018, accepted on 06 Aug 2018 and first published on 06 Aug 2018


Article type: Paper
DOI: 10.1039/C8CP03836H
Citation: Phys. Chem. Chem. Phys., 2018, Accepted Manuscript
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    Conformational Changes of DNA Induced by trans-Azobenzene Derivative via Non-Covalent Interactions

    H. Zhang, H. Fu, X. Shao, C. J. Chipot, A. Monari, F. Dehez and W. Cai, Phys. Chem. Chem. Phys., 2018, Accepted Manuscript , DOI: 10.1039/C8CP03836H

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