Carbazole Derivatives’ Binding to c-KIT G-Quadruplex DNA

Abstract

The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5′-AGGGAGGGCGCTGGGAGGAGGG-3′, derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations. All free carbazole ligands exhibited modest fluorescent properties, but after binding to the DNA the fluorescence intensity increased significantly. The binding affinities of carbazole ligands to the c-KIT 1 DNA were comparable showing values in the order of 105 M−1. Molecular modeling highlights the differences in interactions between each particular ligand and studied G-quadruplex, which potentially influenced binding strength. Obtained results relevant that all three investigated ligands have stabilization properties on studied G-quadruplex.

Binding Study of the Fluorescent Carbazole Derivative with Human Telomeric G-Quadruplexes

“…Similar spectral effects observed in the UV-Vis titration experiments have been previously ascribed to a two-step complex formation between the ligand and G-quadruplex [43,44,73,74,75,76]. The hypochromic effect was observed at lower G4/ligand ratios, when the excess of positively charged ligand could be stacked onto the G-quadruplex surface as a result of electrostatic attraction with phosphate groups leading finally to ligand–ligand aggregation on the G-quadruplex.…”

“…In this paper we report the synthesis of a ( E )-2-(2-(9-(4-(1 H -imidazol-1-yl)butyl)-9 H -carbazol-3-yl)vinyl)-3-ethylbenzo[ d ]thiazol-3-ium ligand 3 , which is capable of stabilizing G-quadruplex structures (Figure 1) [43,44]. The starting 9-(4-(1 H -imidazol-1-yl)butyl)-9 H -carbazole 1 was synthesized from carbazole by a known synthetic procedure in 62% overall yield [65].…”

“…The 9-N-substituted carbazole derivatives were found to interact with G-quadruplexes via external stacking thanks to the presence of a planar carbazole unit and a vinylbenzothiazolium arm coupled with delocalized π-electrons [43,44,45]. The C=C double bond structural element of the ligand offered the opportunity of controlling the ligand structure by light ( cis-trans photoisomerization), similarly as for the arylstilbazolium ligands [72].…”

“…Since the first reports on G-quadruplex ligand activity (inhibition of human telomerase) [23,24], the number and variety of “G-quadruplex ligands” has increased rapidly over the years [2,3,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45]. Among them are derivatives of carbazole, for example 3,6-bis[2-(1-methylpyridinium)vinyl]carbazole (BMVC) [33,34,35,36], benzimidazole‒carbazole ligands [37,38,39] and others [40,41,42,43,44,45]. Carbazole derivatives have aroused much interest because of their photophysical [46,47,48,49,50,51] and biological properties [52,53,54].…”

“…Recently, we have reported on the stability and interaction of three carbazole ligands with G-quadruplexes formed by sequences corresponding to region of c-MYC NHE III 1 and c-KIT 1 [43,44]. It has been found that introduction of different substituents on the nitrogen atom of carbazole has modest impact on the G-quadruplex binding properties as the relevant ligand demonstrated similar stabilization of G4s and comparable binding affinities in the order of 10 5 M −1 .…”