The interactions of 5-hydroxy-1,4-naphthoquinone with three nucleobases (thymine, cytosine, adenine) and one nucleoside (guanosine), investigated by cyclic voltammetry in aprotic solvent, showed significant change in the redox behavior of the quinone group. Then, the interactions between 5-hydroxy-1,4-naphthoquinone and single-stranded oligonucleotides were studied in phosphate buffer saline solution using a random sequence and homo-oligonucleotides (polyA(20), polyT(20), polyC(20) and polyG(20)). Finally, the interactions of 1,4-benzoquinone and 1,4-naphthoquinone were studied to compare with 5-hydroxy-1,4-naphthoquinone and to propose different interaction modes. The results help to elucidate the transduction mechanism involved in label-free quinone-based electrochemical DNA sensors. (C) 2012 Elsevier Ltd. All rights reserved.