Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View

The origin of genetic material on earth is an age-old, entangled mystery that lacks a unanimous explanation. Recent studies have suggested that noncanonical bases such as barbituric acid (BA), melamine (MM), cyanuric acid (CA), and 2,4,6-triaminopyrimidine (TAP) may have undergone molecular selection within the “prebiotic soup” to spontaneously form supramolecular assemblies, which then covalently assembled into an RNA-like polymer (preRNA). However, information on the role of intrinsic interactions of these candidate heterocycles in their molecular selection as the components of preRNA, and the subsequent transition from preRNA to RNA, is currently missing in the literature. To fill this gap in our knowledge on the origin and evolution of primitive genetics, the present work employs density functional theory (B3LYP-D3) to evaluate and compare the stacking propensities of dimers containing prebiotic noncanonical (BA, MM, CA, and TAP) and/or canonical RNA bases (A, C, G, and U). Our detailed analysis of the variation in stacking strength with respect to four characteristic geometrical parameters between the monomers [i.e., the vertical distance, the angle of rotation, and (two) displacements in the x and y directions] reveals that stacking between nonidentical bases is preferred over identical bases for both prebiotic–prebiotic and canonical–canonical dimers. This not only underscores the similarity between the fundamental chemical properties of preRNA and RNA constituents but also supports the likelihood of the evolution of modern (RNA) genetics from primitive (preRNA) genetics. Furthermore, greater average stacking stabilization of canonical dimers than that of dimers containing one canonical and one preRNA nucleobase (by ∼5 kJ mol–1) or dimers solely containing preRNA nucleobases (by ∼12 kJ mol–1) indicates that enhanced stacking is an important factor that may have spurred the evolution of preRNA to an intermediate informational polymer to RNA. More importantly, our study identifies the central roles of CA, BA, and TAP in stacking stabilization within the preRNA and of BA in stacking interactions within the intermediate polymers and suggests that these heterocycles may have played distinct roles in various stages during the evolution from preRNA to RNA. Overall, our results highlight the significance of stacking interactions in the selection of nucleobase components of preRNA.