The gold electrodes modified with self-assembled monolayers of a 13-mer peptide nucleic acid (PNA) probe and 8-amino-1-octanethiol were used for the detection of a complementary oligonucleotide at a femtomolar level using the ion-channel sensor technique. No response to a one-base mismatched oligonucleotide was observed. The electrode surface was positively charged in a pH 7.0 buffer solution due to the protonation of an amine group of the thiol, where the electron transfer between the positively charged marker [Ru(NH₃)₆]³⁺ and the surface was hindered because of the charge–charge repulsion between them. Binding of the negatively-charged complementary oligonucleotide to the probe cancels the positive charge at the surface, and provides an excess negative charge at the surface, thereby facilitating the access of the marker to the electrode surface and its redox reaction. Using a 13-mer PNA probe for this sensing mode, we achieved the detection of the oligonucleotide at a femtomolar (∼10⁻¹⁵ M) level, improved by five orders of magnitude than the previously used 10-mer PNA probe.