We study the effect that uncertainties in the nuclear spin-dependent structure functions have in the determination of the dark matter (DM) parameters in a direct detection experiment. We show that different nuclear models that describe the spin-dependent structure function of specific target nuclei can lead to variations in the reconstructed values of the DM mass and scattering cross section. We propose a parametrization of the spin structure functions that allows us to treat these uncertainties as variations of three parameters, with a central value and deviation that depend on the specific nucleus. The method is illustrated for germanium and xenon detectors with an exposure of 300 kg yr, assuming a hypothetical detection of DM and studying a series of benchmark points for the DM properties. We find that the effect of these uncertainties can be similar in amplitude to that of astrophysical uncertainties, especially in those cases where the spin-dependent contribution to the elastic scattering cross section is sizable.
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