Abstract DNA and RNA can adopt a variety of stable higher‐order structural motifs, including G‐quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher‐order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher‐order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher‐order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher‐order structures of nucleic acids is also underway. In this personal account, we focus on the following higher‐order structures of nucleic acids, double‐stranded DNA containing the abasic site, T−T/U−U mismatch structure, and G‐quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.
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