Beyond Symmetric Motifs: Asymmetric Small-Molecule Recognition Directs a New Poly(adenine) Assembly

Abstract DNA/small-molecule hybrid materials provide a powerful route to reprogram nucleic acid structures without covalent modification. However, to date only two small molecules have been shown to direct such assemblies, both relying on symmetric hydrogen-bonding faces. Here, we report that 3-methylxanthine (3MeX), a purine-derived molecule with nonequivalent hydrogen-bonding faces, directs the assembly of poly(deoxyadenylic) acid into a new, cooperative arrangement. Through preorganization experiments, systematic modification of small-molecule binding faces, nucleobase engineering, and molecular dynamics simulations, we characterize key hydrogen-bonding interactions governing this structure. We propose a model in which two poly(deoxyadenylic) acid strands associate in an antiparallel arrangement, held together by hydrogen-bonded quartets, each comprising two adenine bases and two 3MeX molecules, similar to the G-quartets of G-quadruplex structures. The assembly exhibits pronounced thermal hysteresis consistent with a cooperative, nucleation–growth mechanism, and forms from a pharmacologically relevant molecule whereby the recognition process is exquisitely sensitive to small-molecule structure. This work establishes a new interaction motif in DNA/small-molecule hybrids, in which asymmetric, multi-face recognition enables new, directional assemblies of unmodified nucleic acids. We show that this interaction can be integrated into DNA nanotechnology to enable small-molecule-triggered dimerization, and higher-order polymerization of DNA nanostructures. The accessibility of this motif under neutral conditions, together with its tolerance to small-molecule modification, points to potential applications in programmable nanomaterials, and nucleic acid–based systems that interface with biological environments.