Recognition Mechanism of Complementary Nucleobases and Sequences in DNA and RNA: Interplay of Watson-Crick Hydrogen Bond Formation and Base Stacking Interactions

A/T(U) and G/C nucleobase pair formation in DNA and RNA are crucial to numerous fundamental biological processes, including replication, transcription, and translation. The specificity of A/T(U) and G/C base pairing is used to recognize complementary sequences in medical and biotechnological applications, such as PCR, nucleic acid drugs, and CRISPR–Cas9-based gene editing. To understand the fidelity of biological reactions and improve the accuracy and efficacy of applications, particularly by avoiding off-target binding, clarifying the mechanism of recognition of complementary bases or sequences is essential. Despite the prevailing view that Watson-Crick hydrogen bonding is a primary mechanism for complementary base recognition, several experiments have shown that DNA polymerase does not require hydrogen bonding to select complementary bases. Other factors—such as the geometry of bases and base stacking—appear to be involved in the selection. Artificial base pairs lacking hydrogen bonds but recognized by DNA polymerase were successfully designed solely based on base-pair geometry. However, hydrogen bonding also contributes to recognition. Furthermore, the accuracy of selecting a complementary nucleobase or sequence varies across reactions, suggesting the existence of multiple selection mechanisms. This review provides an overview of biological processes and applications involving base pairing and discusses the molecular mechanism underlying complementary base recognition.