RNA G-quadruplex structure recognition by chimeric peptides

G-quadruplexes (G4s) are non-canonical nucleic acids involved in gene regulation and have attracted interest as potential therapeutic targets. However, developing ligands that selectively recognize specific G4 structures remains challenging. Here, we report the rational design of chimeric peptides that combine a de novo selected peptide (Pep11) with a native peptide (Rhau18) derived from the endogenous DHX36 protein. The chimeric peptides bound RNA G4s (rG4s) with nanomolar affinity, representing a 10-fold enhancement over the individual modules, while retaining selectivity for rG4s over DNA G-quadruplexes (dG4s) and non-G4 RNA structures. These chimeric peptides inhibit telomerase activity in vitro and suppress the translation of an rG4-containing reporter gene in living cells. Live-cell imaging further supports their ability to recognize rG4 structures in a cellular context. Molecular dynamics (MD) simulations of the peptide-rG4 complexes were consistent with the experimental observations and suggested that peptide fusion promoted a more extensive and persistent peptide-rG4 interface, providing a possible structural basis for the enhanced binding affinity. Overall, our study suggests that chimeric peptide design provides a useful strategy for developing selective rG4-targeting ligands and modulating functional nucleic acid structures.