G-quadraplex (G4) are a four-stranded DNA or RNA structure, formed in guanine rich sequences of DNA or RNA.¹ In these regions, guanine bases can form Hoogsteen hydrogen bonding to give G-tetrads, which are stacked with a physiological relevant cation (Na⁺, K⁺ or Ca²⁺) to give the G4 structure. It has been shown that G4 structures can be responsible for the regulation of certain oncogenes.² It was recently demonstrated by the group of Balasubramanian, that there are approximately 10,000 G4 structures in human chromatin using immunoprecipitation and ChIP-seq.³

The stabilisation of G4 DNA with small molecules are promising strategy for the treatment of cancer.⁴ The first example of small molecules (porphyrin) targeting G4 and leading to the down regulation of the c-Myc protooncogene was reported by Hurley and co-workers.⁵ More recently, the same group reported GQC-05, an ellipticine derivative, which was found to also down regulate c-Myc, upon binding to the upstream G4.⁶

In this work, a series of new G4 ligands or probes, derived from multicarbazoles are reported. Using a palladium-catalysed Suzuki-Miyaura cross-coupling reaction, 1,3,5-tri(carbazole-3-yl)benzene was prepared from 3-bromocarbazole and 1,3,5-phenyltribornic acid, pinacol ester with a reasonable yield. Further functionalisation of the carbazole with amine side chains was achieved by nucleophilic substitution with chloro-alkylamines. Crystal structure of 1,3,5-tri(carbazole-3-yl)benzene shows that the carbazole moieties π-stack with other carbazoles on different molecules, suggesting the possibility of a π-stacking mechanism with guanine bases.

After purification,  the compounds were characterised and then tested using a variety of techniques to determine binding affinity of ligands to G4 DNA. Compounds are tested with Forster resonance energy transfer (FRET) melting, to determine how well compounds can stabilise G4 structures. Competition assays with G4 and dsDNA will also be performed to determine the specificity these compounds have for G4 over duplex DNA.