In the context of the origin of life, clays have been proposed as possible materials to adsorb, protect and potentially foster the formation of complex bio molecules. In the present study, the adsorption of nucleotides onto clay surfaces has been tackled through classical molecular dynamics calculations. Various parameters have been varied by modelling the deoxyguanosine mono phosphate molecule at the basal surface of two clay minerals: montmorillonite and nontronite, at pH = 3 and 7, and in a 0.5 M NaCl solution in presence or absence of Ca²⁺ divalent cations. It has been firstly observed that counter cations in solution adopts a three-layers structure above the mineral basal surfaces which can be modified by the mineral composition, the location of the surface charge, and results in substantial effects on nucleotide adsorption. For montmorillonite, for which the charge is located in the octahedral (inner) layer, the two closest counter cations layers above the mineral surface are less populated while the third layer comprises the largest cations density. For nontronite, for which the negative charge is located on the surface oxygen atoms of the tetrahedral layer in contact with the aqueous solution, the first two counter cations layers are the most populated. The negative charge on the surface is thus screened by the first two layers above nontronite surface, and by only the third layer for montmorillonite. As a result, the negatively charged phosphate moiety of nucleotides can approach closer to the surface of nontronite by coordinating with the first two layers cations and the nucleobase adsorb on the surface in a parallel orientation maximizing Van der Walls interactions. On montmorillonite, the phosphate coordinates the cations of the third layer and thus remains rather far from the surface, which does not allow the nucleobase parallel binding. These theoretical results explain experimental results on the effect of mineral and solution composition on the adsorption of nucleotides on the surface of swelling clays.