The rate of a chemical reaction can be sensitive to the isotope composition of the reactants, which provides also for the sensitivity of such “spin-sensitive” reactions to the external magnetic field. Here we demonstrate the effect of the external magnetic field on the enzymatic DNA synthesis together with the effect of the spin-bearing magnesium ions ($$^{25}$$
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Mg). The rate of DNA synthesis monotonously decreased with the external magnetic field induction increasing in presence of zero-spin magnesium ions ($$^{24}$$
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Mg). On the contrary, in the presence of the spin-bearing magnesium ions, the dependence of the reaction rate on the magnetic field induction was non-monotonous and possess a distinct minimum at 80–100 mT. To describe the observed effect, we suggested a chemical scheme and biophysical mechanism considering a competition between Zeeman and Fermi interactions in the external magnetic field.