Exploring the stabilizing effect on the i-motif of neighboring structural motifs and drugs

Cytosine-rich DNA sequences may fold into a structure known as i-motif, with potential in vivo modulation of gene expression. The stability of the i-motif is residual at neutral pH values. To increase it, the addition of neighboring moieties, such as Watson-Crick stabilized loops, tetrads, or non-canonical base pairs have been proposed. Taking a recently described i-motif structure as a model, the relative effect of these structural moieties, as well as several DNA ligands, on the stabilization of the i-motif has been studied. To this end, not only the original sequence but different mutants were considered. Spectroscopic techniques, PAGE, and multivariate data analysis methods have been used to model the folding/unfolding equilibria induced by changes of pH, temperature, and the presence of ligands. The results have shown that the duplex is the moiety that is responsible of the stabilization of the i-motif structure at neutral pH. The T:T base pair, on the contrary, shows little stabilization of the i-motif. From several selected DNA-binding ligands, the G-quadruplex ligand BA41 is shown to interact with the duplex moiety, whereas non-specific interaction and little stabilization has been observed within the i-motif.

Automated summary

Cytosine-rich DNA sequences can form i-motif structures, which have the potential to modulate gene expression in vivo. The stability of i-motif structures is low at neutral pH, but can be increased by adding neighboring moieties or DNA ligands. This study investigated the relative effects of these structural moieties and ligands on i-motif stabilization using spectroscopic techniques and multivariate data analysis methods. The results showed that the duplex is responsible for stabilizing the i-motif structure at neutral pH, while the T:T base pair has little effect. Among the selected DNA-binding ligands, the G-quadruplex ligand BA41 interacts with the duplex but shows little interaction and stabilization within the i-motif.