Biorecognition and biocatalytic reactions of DNA monolayers, such as hybridization, polymerization, and hydrolytic digestion, were followed in situ by chronocoulometry and Faradaic impedance spectroscopy. Hydrophobic magnetic nanoparticles attracted to, and retracted from, the electrode surface by an external magnetic field were used to activate and inhibit the DNA-monolayer reactions, respectively. The attraction of the magnetic nanoparticles to the electrode surface generated a hydrophobic thin film on the surface that is not permeable for the water-soluble components required for the DNA-monolayer reactions. This results in the inhibition of the DNA-monolayer reactions. The retraction of the magnetic nanoparticles from the surface regenerated the free nucleic acid-functionalized surface that was exposed to the aqueous solution, thus reactivating the DNA-monolayer reactions. The reversible inhibition and activation of the DNA-monolayer reactions upon the cyclic attraction-retraction of the hydrophobic magnetic nanoparticles may be used to synthesize programmed DNA chips.