Coarse-Grained Model for Sequence-Dependent Adsorption of ssDNA on Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) have extraordinary properties due to their symmetry, high aspect ratio, and thermal conductivity, all of which make them attractive toward many applications in medicine, nanotechnology, electronics, optics, and other fields. ssDNA is known to form stable dispersions of SWCNTs, and depending on its sequence can remarkably enable separation of SWCNTs of a particular chirality. In this work, we use a minimalist coarse-grained simulation model to explore general aspects of the sequence-dependent interaction of ssDNA with SWCNTs. Oligomeric chains of guanine and thymine nucleobases were investigated, revealing a significant difference in the thermodynamic behavior of three investigated sequences. G(12) was found to adsorb most readily owing to the strong and stable stacking interactions between its bases and the nanotube surface. On the other hand, the smaller thymine bases allow the T-12 chains to form stacking interactions between neighboring bases as well as with the nanotube simultaneously. (GT)(6) interacts most weakly with the SWCNT and reveals a greater sensitivity toward nanotubes with different radii, in contrast to the homo-oligomers. The uniqueness of each sequence is attributed to geometric as well as energetic differences between neighboring bases.