Binding of Harmine Derivatives to DNA: A Spectroscopic Investigation

Abstract

Harmine belongs to a group of β-carboline alkaloids endowed with antitumor properties. Harmine and its derivatives are thought to bind to DNA and interfere with topoisomerase activities. We investigated the base-dependent binding of harmine, and three of its synthetic anticancer-active derivatives to the genomic DNA from calf thymus and two synthetic 20-mer double helices, the poly(dG-dC)·poly(dG-dC) and the poly(dA-dT)·poly(dA-dT), by means of UV-Vis and circular dichroism (CD) spectroscopies. The data show that the DNA binding and stabilising properties of the investigated derivatives are base pair-dependent. These results could be used as a guide to design and develop further bioactive analogues.

Keywords: DNA duplex; alkaloids; spectroscopy.

Figure 1

Chemical structure of harmine (7-methoxy-1-methyl-9H-pyrido(3,4-b)indole), and its synthetic derivatives: I (4-methoxy-1-methyl-9H-pyrido(3,4-b)indole), II (4-methoxy-1,9-dimethyl-9H-pyrido(3,4-b)indole), and III (3-benzyl-1-methoxy-6-oxo-6H-indole[3,2,1-de]-[1,5]-naphthyridinin-3-ium bromide).

Figure 2

Normalised UV-Vis thermal melting profiles of Calf thymus DNA (ctDNA) at increasing [HR]:[ctDNA]_bp ratio (a); and at [ligand]:[ctDNA]_bp of 0.50 (b). The ligand concentrations were increased over a fixed (ctDNA)_bp. Melting curves were obtained monitoring the absorbance at 260 nm as a function of temperature.

Figure 3

UV absorption spectra of the ctDNA with (a) harmine; (b) I; (c) II; and (d) III. The arithmetical ligand-ctDNA sum spectra are reported as well.

Figure 4

Normalised UV thermal denaturation curves of d(GC)₁₀ (a) and d(AT)₁₀ (b) in the absence and presence of ligands at 0.50 [ligand]:[DNA]_bp ratio followed at 260 nm.

Figure 5

Circular dichroism spectra of (a) ctDNA; (b) d(GC)₁₀; and (c) d(AT)₁₀, either free or as bound at 0.50 [ligand]:[DNA]_bp ratio to the harmine or its three derivatives.