Plasmid DNA (pDNA) purification has been extensively investigated for various biological and biochemical applications such as transfection, polymerase chain reaction and DNA therapeutics. In the previous paper, we have described the synthesis, characterization and evaluation of microbeads (“Amikabeads”) derived from aminoglycoside amikacin for pDNA binding via anion-exchange chromatography. Here, we investigated the pDNA binding performance of conjugating Amikabeads with two highly specific DNA binding ligands via minor groove hydrophobic interaction. The pDNA maximum binding capacity of doxorubicin drug-conjugated Amikabeads (“doxo-beads”) was found out to be 429 μg pDNA/ mg of doxo-beads with a Langmuir constant of 8.21*10-4 L/mg, whereas the binding performance of berenil drug-conjugated "mikabeads (“berenil-beads”) was 142 μg pDNA/mg of berenil-beads with a adsorption constant of 4.71*10-5 L/mg. In addition, the desorption percentage of doxo-beads and berenil-beads was obtained as 52% and 41%, respectively. Our results indicate that by conjugating with highly specific DNA binding ligands, Amikabeads-drug complex enhances the pDNA binding performance and contains a promising potential for future applications in biotechnology field.