Ligand Selectivity by Inserting GCGC-Tetrads into G-Quadruplex Structures

G-Quadruplexes (G4s) assembled from tandem G-rich repeat sequences exhibit significant biological functions and applications, which may well depend on their structural features, such as the planar arrangement of G-tetrads and flexibility of loop regions. It has been found that cytosine-intercalated G-repeat sequences also assemble to be quadruplex structures, involving the formation of nonplanar GCGC-tetrads. Herein, to investigate the effect of GCGC-tetrads on structural properties of G4s, some previously studied quadruplexes with or without GCGC-tetrads were selected, and were used to interact with various developed G4 ligands. Our data show that stacked G-tetrads in quadruplexes are important for the π-π stacking interactions, thus promoting the combination with end-stacking ligands, such as porphyrins or planar small molecules. This is confirmed by the observation that the quadruplex formed by d(GGGCT₄ GGGC) with two internal G-tetrads and two external GCGC-tetrads can bind to planar ligands in the presence of specific G4-stabilizing cations, including K⁺ and Pb²⁺ , and can realize the sensitive detection of Pb²⁺ . However, the quadruplex composed of two external G-tetrads and two internal GCGC-tetrads formed by d(GCGGT₃ GCGG) facilitates the binding of nonplanar ligands, such as triphenylmethane (TPM) dyes, owing to the structural flexibility induced by internal GCGC-tetrads. This work provides new insights into the interaction between DNA quadruplexes and specific ligands, which is beneficial to the development of quadruplex-based biosensors and the design of anticancer drugs.