Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations
We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxyribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, each consisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 and T12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surface occurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strong chemical bonding between the terminal phosphate group and the anatase surface. The interactions between the nucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinity for the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more strongly when the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidic conditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy. Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surface and comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2 interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimal nanoconjugates for their specific final goals and applications.