Abstract

G-quadruplex (G4) DNA structures are secondary structures of DNA that are involved in central biological processes but also linked to human diseases such as cancer. There are hundreds of thousands of potential G4s in the human genome and specificity between G4s is thus of key importance both to enable chemical biology studies of G4 regulation and function but also to further explore G4 DNA as therapeutic targets. Traditional medicinal chemistry approaches have largely failed to deliver small molecules with individual G4 specificity and alternative approaches are thus required to overcome this challenge. We here present a strategy that utilizes base-complementarity with a sequence adjacent to the target G4 structure. Our presented GL-O strategy is based on a potent but non-specific G4-stabilizing ligand that is conjugated to a guide oligonucleotide sequence with base-complementary to a sequence flanking the target G4 structure (Figure 1). The idea behind this approach is that the oligonucleotide sequence guides the G4-ligand to its target G4 structure, avoiding off-target interactions. We show that conjugation of the guide oligonucleotide sequence to the G4-ligand result in a synergistic effect on both the binding affinity and the stabilization of the target G4. Furthermore, we show that complementarity highly impacts the binding properties of the GL-O and the approach actively decreases the unspecific G4 stabilization (non-target G4s without flanking complementary DNA sequence). The oligonucleotide conjugation thus guides the G4-ligand to the target G4 structure, increase the binding and stabilization of this G4 structure, and prevent off-target interactions. In conclusion, our proposed strategy merges the design and development of G4-ligands with the significant developments in oligonucleotide-based therapeutics, which might have direct value as a novel therapeutic modality but also to explore G4 biology.