Structural basis of Bis-quinolinium scaffolds binding to Quadruplex-duplex hybrids from PIM1 oncogene

This study investigates the interactions of two bis-quinolinium ligands, Phen-DC3, and 360A, with G-quadruplex-duplex hybrids (QDHs), focusing on the different QDH constructs from the PIM1 oncogene. Using solution NMR spectroscopy and molecular dynamics simulations, we show that both ligands selectively bind the hybrid QDH conformation while exhibiting negligible affinity for the antiparallel topology. High-resolution NMR structures reveal that both ligands localize at the G-quadruplex-duplex (Q-D) junction but with distinct binding dynamics. Our results indicate that ligand binding specificity depends on factors such as ligand structure and the Q-D interface's integrity rather than the base pair's nature or the length of the lateral duplex domain. Stable capping structures, such as the G-C-G-C quartet in antiparallel PIM1 QDH, hinder specific binding with high affinity. Notably, a single Watson-Crick base pair in the lateral loop, stacked with the G-tetrad, suffices for accommodating bis-quinolinium ligands. The strong binding affinity and specificity of Phen-DC3 and 360A for hybrid QDHs in the Xenopus laevis oocytes suggest their potential for selectively targeting QDH structures under complex cellular environments. Our findings offer valuable insights into conformational fluctuations of G-rich sequences using small molecule-based ligands for therapeutic, biotechnological, and nanotechnology applications.