In this work, DNA-Hg(II). interactions were investigated by monitoring the translocation. of DNA, hairpins in a protein ion channel in the absence and presence of metal, ions. Our experiments demonstrate that target specific hairpin structures :could be Stabilized,much more significantly by mercuric ions than by the stem length and the loop size of the hairpin due to the formation of Thymine-Hg(II)-Thymine complexes. In addition, the designed DNA probe allows the development of a highly sensitive nanopore sensor for Hg2+ with a detection limit of 25 nM. Further, the sensor is specific, and other tested metal ions including Pb2+, Cu2+, Cd2+, and so on with concentrations of up to 2 orders of magnitude greater than that of Hg2+ would not interfere with the mercury detection.