Boronate affinity systems have been recently used for the specific isolation of cis-diol group carrying biomolecules such as glycoproteins, nucleosides, carbohydrates. Nanosized materials have been extremely used for the biotechnological purposes due to their unique properties and their high surface areas. The objective of this presented work was to develop a new boronate affinity system for the nucleoside adsorption. For this purpose, poly(HEMA) nanoparticles were synthesized by using surfactant free emulsion polymerization technique and then functionalized with phenylboronic acid. Synthesized nanoparticles were characterized with FTIR, SEM, and Zeta size analysis. Nucleic acid adsorption experiments were repeated for different medium pH values, for various nucleosides concentrations, for different temperatures and ionic strengths, in order to determine the optimum adsorption conditions. In the light of these studies, it can be concluded that this boronate ligand carrying nanoparticles were very valuable for the separation of nucleosides.