DFT Reveals Adenine Adsorption on Graphene Oxide and AuNPs: A Potential Reason for Failure in Aptamer Selection

With the advancement of aptamer, an increasing number of SELEX methods have been developed. However, not all methods can effectively and efficiently enrich aptamer sequences. Recent studies have shown that GO-SELEX and Gold-SELEX methods barely enrich adenosine aptamers, likely due to the adsorption of adenosine on the surfaces of GO and AuNPs. In this study, we used density functional theory to investigate the adsorption behavior and strength of adenine, the nucleobase of adenosine, on Au clusters, GO clusters, and rGO clusters. Adenine exhibited the highest adsorption energy on Au clusters at -1.3676 eV, followed by GO at -0.6146 eV, and the weakest on rGO at -0.5966 eV. Furthermore, by analyzing Mayer bond order, charge transfer, IGMH, and energy decomposition analysis, we determined that adenine interacts with Au clusters mainly through coordination bonds, Au-π interactions, and van der Waals forces; with GO clusters via hydrogen bonding, π-π stacking, and van der Waals forces; and with rGO clusters through π-π stacking and van der Waals forces. We find that adenine adsorption is strongest on Au clusters, weaker on GO, and weakest on rGO. This suggests that during SELEX, adenosine strongly adsorbs to the substrate, making it largely unavailable in solution to perform its selective role, thereby causing the failure in aptamer enrichment. These findings indicate that the interaction between the target and the SELEX substrate significantly affects SELEX efficiency. We recommend that future studies thoroughly consider such interactions.