Structure and the energy of base pairing in non-natural bases of nucleic acids: the azaguanine–cytosine and azaadenine–thymine base pairs

Watson–Crick optimized geometries and the energies of base pairing for the natural pairs of nucleic bases: adenine–thymine (AT) and guanine–cytosine (GC) have been recalculated by ab initio methods in order to compare results to those found for the non-natural azaadenine–thymine (AAT) and azaguanine–cytosine (AGC) pairs. Geometry optimizations carried out at the HF/6-31G** level and energies obtained at MP2/6-31G**, show that AAT and AGC have hydrogen bonding patterns similar to the natural AT and GC and that the interaction energies (ΔH0int) for the former are ca. 7 kcal/mol more stable than the latter. Accordingly, the pairs based on azapurines would be favored with respect to the natural pairs. Some possible explanations why nature does not use extensively the azabases in base pairing are given.