MW NPs represent one of the current most suitable alternatives to antibodies for molecular recognition and diagnostic applications. Here we present the synthesis of MIP NPs imprinted for 2'-deoxyadenosine (dA) prepared using for the first time a modified polymerizable 2'-deoxyuridine complementary residue. We demonstrate that the introduction of this modified monomer results in an increase of the affinity of the produced MIP NPs, without altering their physical properties such as size, shape, or dispersibility. The imprinted NPs have shown the ability to specifically recognize dA, whereas no imprinting effect was observed for 2'-deoxyguanosine (dG) or deoxycytidine (dC). The results suggest that such monomers (and their phosphoramidites) could be used in the synthesis of oligomer or longer DNA sequences for potentially producing hybrid MIP DNA materials with improved recognition performance.