Preferential targeting of i-motifs and G-quadruplexes by small molecules

Abstract

I-motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands (PBP1 and PBP2) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs have been synthesized using a modular method involving Cu(I)-catalyzed azide and alkyne cycloaddition. The para-isomer, PBP1 exhibits high selectivity for i-motifs while the meta-isomer PBP2 binds selectively to G-quadruplex structures. Interestingly, these ligands have the ability to induce the G-quadruplex or i-motif structures from the unstructured single-stranded DNA conformations as observed by single molecule Förster resonance energy transfer (smFRET) studies. The quantitative real-time polymerase chain reaction (qRT-PCR), western blot and dual-luciferase assays indicate that PBP1 upregulate and PBP2 downregulate BCL-2 gene expression in cancer cells.