We present the first theoretical study of molecular recognition of systems interacting via multiple sites, using the density response functions. The model, so-called, localized reactive model derived on the basis of these functions, has been employed for studying the interactions between Watson-Crick type DNA basepairs and the effect of substitution of various groups in the adenine-uracil base pairs. The estimated interaction energies for these base pairs agree remarkably with the corresponding literature and experimental values. It confirms the applicability of the present model to such complex multiple-site interaction cases and can be used as potential predictive tool for the understanding of such general molecular interaction or recognition processes.