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Two maltol-based ligands, <i>N</i>,<i>N</i>&#8242;-bis((3-hydroxy-4-pyron-2-yl)methyl)-1,4-piperazine (<b>L1</b>) and <i>N</i>,<i>N</i>&#8242;,<i>N</i>&#8242;-tris((3-hydroxy-4-pyron-2-yl)methyl)-<i>N</i>-methylethylendiamine (<b>L2</b>), were synthesized and characterized. <b>L1</b> and <b>L2</b>, containing, respectively, two and three maltol units spaced by a diamine fragment, were designed to evaluate how biological and binding features are affected by structural modifications of the parent compound malten. The acid-base behavior and the binding properties towards transition, alkaline-earth (AE) and rare-earth (RE) cations in aqueous solution, studied by potentiometric, UV-Vis and NMR analysis, are reported along with biological studies on DNA and leukemia cells. Both ligands form stable complexes with Cu(II), Zn(II) and Co(II) that were studied as metallo-receptors for AE and RE at neutral pH. <b>L1</b> complexes are more affected than <b>L2</b> ones by hard cations, the <b>L1</b>-Cu(II) system being deeply affected by RE. The structural modifications altered the mechanism of action: <b>L1</b> partially maintains the ability to induce structural alterations of DNA, while <b>L2</b> provokes single strand (nicks) and to a lesser extent double strand breaks of DNA.