Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide

Abstract

The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A₁₂, C₁₂, G₁₂, and T₁₂) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide–GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T₁₂) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T₁₂ was more likely to form a quasi-parallel structure with GO compared to A₁₂, C₁₂, or G₁₂. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T₁₂ and the GO surface enabled T₁₂ to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.