Simultaneous recognition of nucleobase and sites of DNA damage: Effect of tethered cation on the binding affinity

Background: The 3,5-diamino-N-(3-aminopropyl)-6-chloropyrazine-2-carboxamide (DCPC-NH₂) has been synthesized and characterized by Mass and ¹H NMR. The selective binding of the ligand to thymine (T) target base is investigated by the melting temperature (T_m) and fluorescence measurements. Methods: Thermal denaturation study of DNA duplex containing T target base revealed the ΔT_m of 5.1 °C, while least influence was observed for other target bases. The fluorescence of the ligand DCPC-NH₂ is quenched only upon adding the DNA containing T target base. Results: The binding constant for the interaction of the ligand to T target base containing DNA duplex was determined to be 4.7 (± 0.3) × 10⁶ M^{- 1}. The tethered cation in the ligand is found to enhance the binding constant. The ligand binds to both a target nucleotide and an AP site on the complimentary strand for the target strand in a DNA duplex. General significance: Interestingly, the electronic behavior of the ligand depends on the bases flanking the AP site. Its fluorescence is quenched with guanine flanking bases, while it is enhanced with DNA duplex containing T bases flanking an AP site. Finally, the binding modes were visualized by molecular modeling.