Structural Differences at Quadruplex‐Duplex Interfaces Enable Ligand‐Induced Topological Transitions

Abstract Quadruplex‐duplex (QD) junctions, which represent unique structural motifs of both biological and technological significance, have been shown to constitute high‐affinity binding sites for various ligands. A QD hybrid construct based on a human telomeric sequence, which harbors a duplex stem‐loop in place of a short lateral loop, is structurally characterized by NMR. It folds into two major species with a (3+1) hybrid and a chair‐type (2+2) antiparallel quadruplex domain coexisting in a K⁺ buffer solution. The antiparallel species is stabilized by an unusual capping structure involving a thymine and protonated adenine base AH⁺ of the lateral loop facing the hairpin duplex to form a T·AH⁺·G·C quartet with the interfacial G·C base pair at neutral pH. Addition and binding of Phen‐DC₃ to the QD hybrid mixture by its partial intercalation at corresponding QD junctions leads to a topological transition with exclusive formation of the (3+1) hybrid fold. In agreement with the available experimental data, such an unprecedented discrimination of QD junctions by a ligand can be rationalized following an induced fit mechanism.