A computational investigation of the interaction between As³⁺ and deoxynucleotides

A successful aptamer biosensor for As³⁺ in aqueous solution indicated that deoxynucleotides could be a potential ligand for arsenic absorption. However, the interaction mechanism between aptamer and As³⁺ is still not clear. In this paper, a density functional method was applied to investigate the interactions between As³⁺ and four kinds of deoxynucleotides in different charge states. According to the binding energy, dGMP was the best monomer with four different binding modes, and dGMP^3–As³⁺ with the O atom in the phosphate group was calculated to be the most stable one. Moreover, the interaction energy increased when the charge of deoxynucleotide was increased, suggesting that a negative charge was advantageous for deoxynucleotides to absorb As³⁺. The atoms in molecules (AIM), localised orbital locator (LOL) and Charge decomposition analyses (CDA) confirmed that the bond between N atoms and As³⁺ were covalent interactions and that between O atoms and As³⁺ were dominated by electrostatic interactions. As the charge grew, the bond strength of both interactions increased. At the same time, O atom in the vicinity of nucleobases began to participate in the interaction with As³⁺, which was originally bonded to N atoms.