In this review, we have summarized the research effort into the development of unnatural base pairs beyond standard Watson–Crick (WC) base pairs for synthetic biology. Prior to introducing our research results, we present investigations by four outstanding groups in the field. Their research results demonstrate the importance of shape complementarity and stacking ability as well as hydrogen-bonding (H-bonding) patterns for unnatural base pairs. On the basis of this research background, we developed unnatural base pairs consisting of imidazo[5′,4′:4.5]pyrido[2,3- d ]pyrimidines and 1,8-naphthyridines, i.e. , Im : Na pairs. Since Im bases are recognized as ring-expanded purines and Na bases are recognized as ring-expanded pyrimidines, Im : Na pairs are expected to satisfy the criteria of shape complementarity and enhanced stacking ability. In addition, these pairs have four non-canonical H-bonds. Because of these preferable properties, ImN^N : NaO^O , one of the Im : Na pairs, is recognized as a complementary base pair in not only single nucleotide insertion, but also the PCR.