ssDNA TRANSLOCATION WITH CARBOXYL-MODIFIED TRANSMEMBRANE SINGLE-WALLED CARBON NANOTUBE

Abstract

Functionalized transmembrane carbon nanotube (CNT) interactions are of significant importance in CNT-based drug delivery systems and biomedical devices. In this work, an all-atom molecular dynamics simulation is applied to study the encapsulation of a short single-stranded DNA (ssDNA) oligonucleotide in functionalized carbon nanotube (f-CNT) channels. We show that while the van der Waals (vdW) interaction between the ssDNA and the f-CNT induces a spontaneous encapsulation of the molecule within the nanotube channel, the vdW interaction between the ssDNA and biomembrane counteract the encapsulation. However, the vdW attraction due to the f-CNT is stronger than that from the membrane lipid bilayer, leading to the final encapsulation. In particular, we obtain the vdW interaction force between the ssDNA, biomembrane and the f-CNT analytically through a general mathematical model. This interaction force is found to play a dominate role in the adsorption process. The analytically obtained vdW force and potential fields show good correspondence with the adsorption conditions and the adsorption behavior of the ssDNA obtained numerically via the all-atom molecular dynamics simulation.