Abstract
The adsorption characteristics and moving through nanopores of a single-stranded deoxyribonucleic acid (ssDNA) molecule on monolayers, such ashexagonal boron nitride and graphene nanosheets, were studied using the continuous approach with the 6–12 Lennard–Jones potential function. The ssDNA molecule is assumed to be at a distance l above the sheet, and the relation between the minimum energy location and the perpendicular distance of the ssDNA molecule from the nanosheet surface is found. In addition, by assuming that there is a hole in the surface of the nanosheet as a pore, the interaction energies for the ssDNA molecule moving through the pore in the surface of the nanosheet (used to calculate the radius p of the hole) are obtained, which provides the minimum energies. Furthermore, a comparative study with graphene was performed in order to compare with hexagonal boron nitride nanosheets. Our results indicate that the binding energies of the ssDNA onto graphene and hexagonal boron nitride nanosheets are approximately 15.488 and 17.582 (kcal/mol), corresponding to perpendicular distances of l=20.271 and l=20.231 Å, respectively. In addition, we observe that the ssDNA molecule passes through graphene and hexagonal boron nitride nanopores when the gap radius p>7.5 Å. Our results provide critical insights to understand and develop the interactions and translocation of DNA molecules with and through nanosheets.
Highlights
Due to their geometric and mechanical properties and small size, nanomaterials have been utilised in multiple fields, including commercial, biomedical, clean energy, gas storage, genetics, and drug delivery [1,2,3,4,5]
Our results demonstrate that the locations of the single-stranded deoxyribonucleic acid (ssDNA) molecule where the minimum energy occurs were equal to 15.489 and 17.582 corresponding to l ≈ 20.271 and 20.231 Å, as measured from the centre of the helix for GRA and Hexagonal Boron nitride (h-BN), respectively
By comparing the results of the interaction energies between the ssDNA molecule and the h-BN and GRA nanosheets, we found that the interaction energy with h-BN was stronger than those between ssDNA and GRA, as h-BN showed the lowest minimum energy
Summary
Due to their geometric and mechanical properties and small size, nanomaterials have been utilised in multiple fields, including commercial, biomedical, clean energy, gas storage, genetics, and drug delivery [1,2,3,4,5]. Lin et al examined the adsorption of DNA nucleobases (guanine, G; adenine, A; thymine, T; and cytosine, C) on a hexagonal boron nitride nanosheet using the Vienna ab initio Simulation Package (VASP) [14] They showed that the adsorption energies is in the region from 0.5–0.69 eV, in the order of G > A > T > C, which might be due to the different of atoms of nucleobases. We note that the use of the Lennard–Jones (L-J) potential is justified in this case, as the dominant forces present within the interaction energies are van der Waals forces, where this method allows for determination of the potential energy between the interacting molecules as integrals over the volume or surface These integrals can be obtained, in terms of special functions, such as the hypergeometric function F(b∗, c∗; d∗; δ∗), which is useful for quick calculation of the numerical results [21].
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