The present work is aimed to perform a high-level ab initio computational study of the unnatural covalent bond base pairs, recently designed by Gao and Orgel (Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14837) and Kishi et al. (Angew. Chem., Int. Ed. Engl. 1999, 38, 928; Angew. Chem., Int. Ed. Engl. 2001, 40, 147 1), for a better understanding of the underlying structural and energetic features of their base pair formations and for a demonstrating of how they actually accommodate the DNA double helix architecture. In addition, three new tautomeric forms of the Gao-Orgel covalent pair are found and their shape complementarity is analyzed.