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

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.