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A water-soluble tetraazaperopyrene dye as strong G-quadruplex DNA binder

Hahn, Lena, Buurma, Niklaas Jan and Gade, Lutz H. 2016. A water-soluble tetraazaperopyrene dye as strong G-quadruplex DNA binder. Chemistry - a European Journal 22 (18) , pp. 6314-6322. 10.1002/chem.201504934

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Abstract

The interactions of the water-soluble tetraazaperopyrene dye 1 with ct-DNA, duplex-[(dAdT)12⋅(dAdT)12], duplex-[(dGdC)12⋅(dGdC)12] as well as with two G-quadruplex-forming sequences, namely the human telomeric 22AG and the promotor sequence c-myc, were investigated by means of UV/visible and fluorescence spectroscopy, isothermal titration calorimetry (ITC) and molecular docking studies. Dye 1 exhibits a high affinity for G-quadruplex structures over duplex DNA structures. Furthermore, the ligand shows promising G-quadruplex discrimination, with an affinity towards c-myc of 2×107 m−1 (i.e., Kd=50 nm), which is higher than for 22AG (4×106 m−1). The ITC data reveal that compound 1 interacts with c-myc in a stoichiometric ratio of 1:1 but also indicate the presence of two identical lower affinity secondary binding sites per quadruplex. In 22AG, there are two high affinity binding sites per quadruplex, that is, one on each side, with a further four weaker binding sites. For both quadruplex structures, the high affinity interactions between compound 1 and the quadruplex-forming nucleic acid structures are weakly endothermic. Molecular docking studies suggest an end-stacking binding mode for compound 1 interacting with quadruplex structures, and a higher affinity for the parallel conformation of c-myc than for the mixed-hybrid conformation of 22AG. In addition, docking studies also suggest that the reduced affinity for duplex DNA structures is due to the non-viability of an intercalative binding mode.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Chemistry
Subjects: Q Science > QD Chemistry
Additional Information: This is an open access article under the terms of the Creative Commons At- tribution License
Publisher: WileyBlackwell
ISSN: 0947-6539
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 12 February 2016
Last Modified: 04 Jun 2017 08:56
URI: http://orca-mwe.cf.ac.uk/id/eprint/88121

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