Adenine/adenine contacts defined in the G-quadruplex for highly selective Tb3+ binding

Abstract

The folding of nucleic acids is strongly dependent on metal ions. For example, G-quadruplex (G4) structures are usually determined by the specific K⁺/Na⁺ coordination. However, G4 constructs highly selective to high-valent metal ions (for instance, trivalent metal ions) have not been found due to their strong and nonspecific phosphate backbone interactions. Herein, a higher-order G4 structure with a heptad junction, formed by GGA repeats (for example, GGA8 with eight repeats) of the human c-myb promoter, was found to stoichiometrically recruit three Tb³⁺ ions. The junction binding of Tb³⁺ did not affect the global G4 structure of GGA8 because of its high stability in K⁺. The three context A/A contacts with a proper stacking orientation and an appropriate interbase distance were proved to be the specific binding sites of Tb³⁺ (A/Tb³⁺/A). Other high-valent metal ions were unable to interfere with this specific Tb³⁺ binding, suggesting the potential of GGA8 as an aptamer-like DNA for Tb³⁺. This A/Tb³⁺/A binding was also found in another KRAS promoter G4 structure with the same A/A contact, indicating the potential of Tb³⁺ in selectively probing G4 substructures. This work will also inspire more interest in searching higher-order G4 structures for selectively coordinating high-valent metal ions with the purpose of their identification, enrichment, and recovery.