Aims: To constrain the ionization fraction in protoplanetary disks, we present new high-sensitivity interferometric observations of N$_2$H$^+$ in three disks surrounding DM Tau, LkCa 15, and MWC 480. Methods: We used the IRAM PdBI array to observe the N$_2$H$^+$ J=1-0 line and applied a $chi^2$-minimization technique to estimate corresponding column densities. These values are compared, together with HCO$^+$ column densities, to results of a steady-state disk model with a vertical temperature gradient coupled to gas-grain chemistry. Results: We report two dhp detections for LkCa 15 and DM Tau at the $5 sigma$ level and an upper limit for MWC 480. The column density derived from the data for LkCa 15 is much lower than previously reported. The [N$_2$H$^+$/HCO$^+$] ratio is on the order of 0.02--0.03. So far, HCO$^+$ remains the most abundant observed molecular ion in disks. Conclusions: All the observed values generally agree with the modelled column densities of disks at an evolutionary stage of a few million years (within the uncertainty limits), but the radial distribution of the molecules is not reproduced well. The low inferred concentration of N$_2$H$^+$ in three disks around low-mass and intermediate-mass young stars implies that this ion is not a sensitive tracer of the overall disk ionization fraction.
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