Toward Expanded Genetic Alphabets: Insights into Functionalized Ds–Px Unnatural Base Pairs

Abstract Hydrophobic unnatural base pairs (UBPs) expand the genetic alphabet but the molecular factors governing their stability remain unclear. Herein, we report a quantum chemical study of the unnatural base pair Ds–Px and its 13 variants in a B-DNA environment, previously synthesized by Hirao and co-workers. Base-pair interactions are weak but favorable and primarily dispersion-driven, unlike hydrogen-bond-dominated Watson–Crick pairs. Selected modifications, such as incorporation of an additional nitrogen in the fused ring, modestly enhance electrostatic complementarity. In contrast, π–π stacking interactions are significantly stronger and exceed those of natural stacked pairs. These UBPs present an optimal twist angle that matches the canonical 36° of B-DNA, confirming geometric compatibility. Solvation reduces both pairing and stacking energies but reaches a plateau at high dielectric constants. Overall, these findings demonstrate that Ds–Px-type UBPs are stabilized mainly by dispersion-driven stacking and provide molecular insights for future design of expanded genetic alphabets.