Isolation of G-quadruplex structures from human cells using small molecular probes

Abstract

Guanine rich nucleotide sequences of specific pattern are capable of forming unusual secondary structures called G-quadruplexes (G4s). In silico studies have shown that putative G-quadruplex forming motifs (pG4s) are frequently present in functionally important regions of the genome. But formation of G-quadruplex structures by these pG4s in cells remains elusive. In this study, we made an attempt to isolate intrinsic Gquadruplex structure from human cells using biotinylated quadruplex interacting small organic molecules. The ligands showed significant affinity towards structurally different G4s in vitro. This interaction was observed to be selective towards G4s over duplex DNA. Biotinylated ligands were then used to perform Chromatin immuno-precipitation from human cells to isolate cellular G-quadruplex structures. Even though the ligands showed selective binding to G-quadruplex structures in vitro, the methodology used in this study failed to pull down G4s selectively from cells. This demands the need of alternative approaches to identify cellular G-quadruplexes. The ligands have shown significant inhibition of growth and proliferation of cancer cells. This implicates their potential applications in cancer therapeutics.