Roles of flanking sequences in the binding between unimolecular parallel-stranded G-quadruplexes and ligands

G-quadruplexes attract more and more attention in recent years. Numerous small molecules which can induce or stabilize the formation of G-quadruplexes have been investigated on the purpose of anticancer drug development. As a motif existed in physiological condition, flanking sequences are an important part of G-quadruplexes but the study on the impact of flanking sequences on (G-quadruplex)-ligand binding is rarely reported. In this paper, the effects of flanking sequences on binding affinity between a series of unimolecular parallel-stranded G-quadruplex sequences derived from c-myc oncogene promoter (termed as c-myc G-quadruplexes) and their ligands are discussed in detail. The results showed that the flanking sequences on c-myc G-quadruplexes play key roles in (G-quadruplex)-ligand interaction. When a c-myc G-quadruplex is bound to its ligands, the flanking sequences might form a binding cavity above the terminal G-quartet, which could provide a suitable site for ligands to dock in. Moreover, the bases on flanking sequences could interact with ligand through π-π stacking, and finally form a sandwich-stacking mode (terminal G-quartet, ligand and bases on the flanking sequence). This mode could stabilize the (G-quadruplex)-ligand complex effectively and enhance the binding affinity dramatically. However, flanking sequences are also found to exhibit steric hindrance effect which could impede the (G-quadruplex)-ligand binding.