Specific recognition of napthyridine-based ligands toward guanine-containing bulges in RNA duplexes and RNA-DNA heteroduplexes

Mismatched bulges in nucleic acid constructs are important in the recognition event between biological molecules. Herein, we report that napthyridine dimer 2 is able to specifically bind G-G mismatches in all nucleic acid constructs comprising of RNA-RNA, RNA-DNA and DNA-DNA duplexes. This binding behavior suggests that the binding process primarily occurs between the guanine base pairs and the napthyridine moiety, and is independent of the tertiary structure of the nucleic acid duplexes