Structural Aspects of Split G‐Quadruplexes in Quadruplex‐Duplex Hybrid Systems

Abstract G‐quadruplexes are secondary structures of nucleic acids increasingly employed for biological and also technological applications. Being of particular interest, a structural motif called quadruplex‐duplex (QD) hybrid comprises both a G‐quadruplex and duplex domain. Here, we attempted to engineer a bimolecular quadruplex‐duplex hybrid through dual recognition of a receptor by a target strand with the simultaneous formation of both G‐quadruplex and duplex structures. Three different constructs were designed for the G‐quadruplex receptor, featuring either one, two, or three vacant sites. Addition of the target strand filled the vacancies when simultaneously hybridizing with flanking sequences to form a duplex as shown by NMR studies. Formed QD hybrid constructs either constitute an 11 : 1, 10 : 2, or 9 : 3 split G‐quadruplex system. The 10 : 2 QD construct folds into a non‐canonical V‐loop topology. Remarkably, the latter also accommodates 5’‐overhang residues of the target strand although suggested to impose a steric penalty. Formation of the duplex domain is demonstrated to be critical for the successful formation of the intact G‐quadruplex domain. With the formation of a unique QD junction for detection, the constructs may constitute valuable tools for single strand capturing strategies.