H-bond interactions between arsenite and deoxynucleotides at different pH values: A combined computational and experimental study

Abstract

Deoxynucleotides can be good monomers for arsenite ion-imprinted polymers (IIPs) due to the successful obtainment of aptamers which can specifically recognize arsenite. However, the recognition and interaction mechanism between arsenite and deoxynucleotides is still not clear. In this work, the binding interactions between arsenite and deoxynucleotides (dAMP, dTMP, dGMP, dCMP) as pH changing from 1 to 14 were investigated using density functional theory calculations as well as spectroscopy analysis. dGMP was calculated to have the largest affinity towards arsenite. H3AsO30-dGMP0 binding at phosphate group, H3AsO30-dAMP2-, H3AsO30-dCMP0 and H3AsO30-dTMP2- binding around nucleobase were found to be the most stable complexes. This suggests the optimal pH ranges for binding interactions of dAMP, dCMP, dGMP and dTMP towards arsenite might be 6.10–9.23, 1.00–4.50, 1.00–2.40 and 6.40–9.23, respectively, which agree with UV/VIS experimental results. Reduced Density Gradient method indicated that the binding interactions of arsenite with deoxynucleotides are mainly attributed to hydrogen bonds (H-bond). The strengths of these H-bonds are affected by pH. FT-IR and NMR spectroscopy analysis also provided essential H-bonding information, giving direct evidence to support the computational conclusions.