Spatial Matching Selectivity and Solution Structure of Organic-Metal Hybrid to Quadruplex-Duplex Hybrid.

Abstract

The sequence-dependent DNA secondary structures possess structure polymorphism. To date, studies on\xa0regulated ligands mainly focus on individual DNA secondary topologies, while lack focus on quadruplex-duplex hybrids (QDHs). Here, we design an organic-metal hybrid ligand L 1 Pt(dien) , which matches and selectively binds one type of QDHs with lateral duplex stem-loop (QLDH) with high affinity, while shows poor affinity for other QDHs and individual G4 or duplex DNA. The solution structure of QLDH MYT1L- L 1 Pt(dien) complex was determined by NMR. The structure reveals that L 1 Pt(dien) presents a chair-type conformation, whose large aromatic chair surface intercalates into the G-quadruplex-duplex interface via π-π stacking and backrest platinum unit interacts with duplex region through hydrogen bonding and electrostatic interactions, showing a highly matched lock-key binding mode. Our work provided guidance for spatial matching design of selectively targeting ligands to QDH structures.