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Abstract: Two ligand–intercalator–peptide nucleic acid conjugates (L-NADI-PNAs) have been synthesized. Affinity of these conjugates to their complementary DNAs was found to be affected by Zn2+. The magnitude of this effect could be controlled by a variation of the ligand. Upon binding Zn2+ the L-NADI-PNAs form positively charged ZnL complexes, which interact with the negatively charged DNA backbone. This electrostatic interaction stabilizes PNA/DNA duplexes. It has been found that Zn2+ dependent stabilization takes place only if the ZnL complex has a higher total positive charge than the ligand. Linear correlation has been observed between Zn2+ induced stabilization of PNA/DNA duplexes and difference of charges of the ZnL complex and the ligand. [Copyright &y& Elsevier]