Interaction of hemin with quadruplex DNA

Abstract

A DNA enzyme with peroxidase activity is a G-quadruplex-based DNAzyme formed by hemin and G-quadruplex DNA. Activity of peroxide DNAzymes can be influenced by the structure of quadruplex DNA. In this investigation, the interaction of hemin with T30695 G-quadruplex DNA is evaluated. Molecular dynamic simulation indicates that the binding mode of hemin to G-quadruplex DNA is end-stacking, which is consistent with absorption spectroscopy. Based on fluorescence spectroscopy, hemin ejects thiazole orange from bases of four-strand DNA. Circular dichroism spectra showed that no alteration occurs in this type of DNA structure. Graphical Abstract Peroxidase DNAzyme is formed by hemin and G-quadruplex DNA.

Keywords: DNAzyme; Hemin; Interaction; Peroxidase; Quadruplex.

Graphical Abstract

Peroxidase DNAzyme is formed by hemin and G-quadruplex DNA.

Fig. 1

Absorption spectra of hemin titrated with K⁺ and Na⁺ forms of the quadruplex DNA

Fig. 2

Wavelength of maximum absorption, λ_max (a) and maximum absorption (b) of hemin titrated with K⁺ and Na⁺ forms of the quadruplex DNA

Fig. 3

Fluorescence spectra of thiazole orange in presence of K⁺ (a) and Na⁺ (b) forms of the quadruplex DNA titrated with hemin; inserted figures indicate fluorescence intensity at various concentrations of hemin

Fig. 4

Stern–Volmer plots for quenching of thiazole orange with hemin in presence of K⁺ and Na⁺ forms of the quadruplex DNA

Fig. 5

Circular dichroism spectra of K⁺ and Na⁺ forms of the quadruplex DNA (a), K⁺ form (b), and Na⁺ form (c) in absence and presence of hemin

Fig. 6

VMD snapshots of the G-quadruplex DNA-hemin complex for (left) initial and (right) final conformation resulting from MD simulation

Fig. 7

RMSD plots of the quadruplex DNA before (black) and after (gray) binding to hemin