Computational Insight into Graphene Functionalization for DNA-Sequencing Application: A DFT Approach

Abstract

Most diseases such as cancer, gene mutation or infections among humans are due to DNA nucleotides mis-sequence. Deoxyribonucleic acid (DNA) is vital in life science and its sequence detection is imperative in the field of disease diagnosis, forensic sciences, and genomics systems; making materials design for DNA identification very crucial. Two dimensional materials such as graphene doped with some hetero-atoms have been explored for DNA nucleobase detection, but the role of functional groups remain unclear. This study investigates the influence of functional groups in the discrimination of DNA nucleotides: Adenine(A), Guanine (G), Thymine (T) and Cytosine (C). Herein, we studied how functional groups like carboxylate, nitrile, alcohol, amine, amide, methyl-iodide, aldehyde, methyl fluoride, ketone, methyl-bromide, methyl-chloride, ester, methyl-acid iodide, ether, methyl acid fluoride, methyl-acid chloride, methyl-acid bromide and carboxylic acid improve the adsorption capacity of DNA nucleotides onto graphene sheet. The stable configurations of DNA bases adsorbed onto the graphene surface were investigated using spartan student software and density functional theory (DFT) for quantum chemical calculations. The adsorption energies and band gaps were determined during interaction. Our findings reveal that nine (9) of functional groups namely: Methyl-Carboxylic Acid, Methyl-Ester, Methyl-Ketone, Methyl-Ether, Methyl-F, Methyl-I, Acid-F, Amine and Amide are more promising in the DNA sequencing process based on their appreciable quantum chemical parameters such as highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), chemical hardness and softness as well as electrophilicity index. These functional groups have higher affinity for some specific DNA bases. However, the adsorption energies of functionalized graphene-based material (ranging from -0.5 to -3.0) has underscored the that of pristine graphene-based materials (ranging from -0.1 to -0.3 eV) and this is an indicator that, common practice of doping heteroatoms or semiconductor atoms are not the only reliable approach of enhancing 2D-materials for DNA sequencing application, since functionalized graphene-based materials have the potential of competing with doped non-functionalized nano-sheet and nano pore graphene-based material. The relative adsorption energies hierarchy of nucleotides obtained agrees with previous findings reported in the literature. Our findings confirm the potential of computational methods to predict functionalized graphene’s selectivity in discriminating DNA nucleotides, offering a promising avenue for identifying mutations driving tumour growth, predicting prognosis and guiding targeted therapies tailored to the unique genetic profile of each patients’ disease.