In this work, we presented a highly sensitive, on-chip, DNA-based sensor for detection of stx1 gene from STEC, using gold IDEs enabled by the pre-concertation of MB at the sensor. In this work, we developed a facile method for the specific modification of the sensor IDE with Cht-Au nanocomposite, without affecting the accumulator IDE. This was confirmed using fluorescent techniques. Following this, we demonstrated for the first time that applying OCP to the accumulator IDE significantly improved MB intercalation between dsDNA and therefore allowed a highly sensitive detection. Finally, we established a calibration curve between 100 aM to 1 µM of synthetic target strand and specifically detected chromosomal DNA extracted from overnight bacterial cultures. This work is highly relevant for the development of novel point-of-use devices for rapid pathogens detection and can be further extended to allow multiplex detection in the future by modifying separate electrodes with different probe sequences. In addition, it demonstrates a novel use of the IDE where one comb can be specifically modified with a biorecognition molecule while the other comb can be used for other applications such as molecule accumulation or electrochemical pH control.