DNA-based aromatic zipper fastened by an aromatic stacking interaction

A novel thymidine–methyl red conjugate was synthesized and incorporated into oligodeoxyribonucleotides (ODNs). The ODNs containing the conjugate formed a novel nucleic acid-based structural motif, the aromatic zipper, which fastens via the stacking interactions of aromatic residues that are attached to DNA strands. The aromatic zipper can be used to stabilize structural motifs in nucleic acids and their analogues, such as hairpin structures, by fastening their ends.