Nucleobase pairing in expanded oligourea macrocycle driven by phosphate coordination

The specific recognition and stable pairing of nucleobases in aqueous solution are challenging due to strong competitive solvation effects. Although synthetic hosts based on cationic scaffolds have successfully stabilized base pairs through synergistic electrostatic and hydrophobic effects, whether hydrogen bonding alone, given its high adaptability and programmability, can drive nucleobase pairing remains an open question. Herein, we present a neutral and expanded oligourea macrocycle, H[14]U, which features a preorganized cavity tailored for nucleotides binding. This host first strongly binds the phosphate groups of mononucleotides through up to fourteen hydrogen bonds. Within its confined microenvironment, the macrocycle facilitates the formation of both homodimers (U·U) and, more importantly, biologically relevant heterodimer (A·U). The 1:2 host-guest complexes were comprehensively characterized by a combination of NMR, ITC, MS, and CD spectroscopy. ITC studies revealed high-affinity binding with remarkable positive cooperativity. This work demonstrates that hydrogen-bonding interactions, without electrostatic assistance, are sufficient to drive nucleotide base pairing, offering a new design strategy for artificial systems targeting nucleobase recognition and assembly.