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Issue 35, 2018
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Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions

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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 the A and B forms of DNA, the transition being triggered by transcis isomerization of the photoswitch upon non-covalent intercalation. It was proposed that, in its trans conformation, azobenzene stabilizes the A form of DNA. The structural details and the mechanism upon which trans-azobenzene induces the B-to-A DNA transition remain, however, unclear. In the present work, two possible intercalating modes of trans-azobenzene, from the minor groove and from the major groove, were investigated with all-atom molecular-dynamics simulations. Intercalation from the major groove was found to be the most probable binding mode due to favorable electrostatic and π–π stacking interactions. The free-energy profile associated with 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.

Graphical abstract: Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions

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Supplementary files

Article information


Submitted
16 Jun 2018
Accepted
06 Aug 2018
First published
06 Aug 2018

Phys. Chem. Chem. Phys., 2018,20, 22645-22651
Article type
Paper

Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions

H. Zhang, H. Fu, X. Shao, C. Chipot, A. Monari, F. Dehez and W. Cai, Phys. Chem. Chem. Phys., 2018, 20, 22645
DOI: 10.1039/C8CP03836H

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