Targeting non-conventional quadruplex DNA structures with metal complexes

Abstract

Guanine quadruplexes are tetra-stranded DNA secondary structures that fold in this way due to the ability of guanines to form non-canonical hydrogen bonds. Gquadruplexes (G4s) are present in significant biological regions in the genome of both eukaryotes and prokaryotes. Because of this, G-quadruplexes have attracted great attention as a novel therapeutic strategy in cancer, pathogenic and neurodegenerative diseases. Stabilization of G-quadruplexes via small molecules including cationic heterocyclic molecules and metal complexes can be a potential therapeutic approach to overcome current challenges, such as antimicrobial resistance. According to G4LDB database, many G4 ligands (over 4000 ligands) have been synthesized and studied. However, there is still a lack of G4 ligands to target specific sequences, particularly those that lead to non-conventional G4 structures. One example of a non-conventional G4 is the hybrid quadruplex-duplex in LTR-III promoter in the HIV-1 virus. It has been found that stabilization of LTR-III with small molecules can inhibit the viral activity. In this research, I aim to selectively stabilize the hybrid quadruplex-duplex sequences followed by biophysical characterization to study the effect of hybrid quadruplexduplex ligands on the unusual hybrid G-quadruplex structures including LTR-III and MYT1L sequences. To achieve this aim, I synthesized hybrid metal salphen complexes with different backbones and geometries. Biophysical studies were conducted to assess the thermal stabilities of G4 sequences using FRET melting and FRET competition assays. These studies have shown that substituted metal salphen complexes can selectively bind to the hybrid sequences with higher melting temperatures as compared to the traditional G4s. Further analysis was carried out to understand the effect of binding on the G4 topology using CD spectroscopy. In addition, Fluorescence Indicator Displacement (FID) assays and fluorescence spectroscopy were used to gain further insight into the interactions of the compounds and the non-conventional G4s.