The non-B DNA secondary structure known as G-quadruplex (G4) DNA can form in gene-regulatory regions of the human genome. Organic small molecules, so called G4-ligands, which bind and stabilize G4 DNA structures, have emerged as potential therapeutic agents and as chemical probes to study the cellular functions of these secondary DNA conformations. A major challenge, however, is their lack of selectively recognising different G4 structures, which hampers both their further development as therapeutics and their utility as research tools. This limitation can be addressed by linking the G4-ligand to a guide oligonucleotide, complementary to the flanking sequence of the target G4, a strategy called G4-ligand-conjugated oligonucleotides (GL-Os). Here, the G4-ligand used in the GL-O strategy is investigated by altering its physiochemical properties, including size and charge, and evaluating its potency using biochemical and biological assays. The results reveal a strong influence of the G4-ligand on the conjugates' ability to bind and stabilize the target G4 DNA. In particular, a larger and charged G4-ligand enhances both binding and stabilization of the target. However, increasing the G4-ligand potency may also increase off-target G4 binding, highlighting the need for a balanced G4-ligand potency to ensure high GL-O specificity for individual G4 structures.