Base Stacking and Sugar Orientations Contribute to Chiral Recognition of Single-Walled Carbon Nanotubes by Short ssDNAs

Single-walled carbon nanotubes (SWNTs) possess exceptional physical and optical properties that make them promising for biomedical and engineering applications. Chirality-pure and enantiopure SWNTs are of particular interest. While single-stranded DNAs were shown to differentially bind and sort SWNTs, the underlying mechanism is not well understood. In this study, we used molecular dynamics simulations to investigate the binding of single and multiple DNA nucleotides to two (7,5) SWNT enantiomers, E1 and E2. Our simulations reveal that nucleotide bases stack closer to the surface of the E2 than the E1 enantiomer. Surprisingly, chiral single and dinucleotides did not exhibit enantiomer-dependent preferences in angular orientations on the SWNT surface. However, ATT trinucleotides exhibited differences in preferred orientations and arrangements of sugar atoms when bound to SWNT enantiomers. Our results suggest that preferred arrangements of DNA sugar moieties may be an important parameter that contributes to the differential binding of DNAs to SWNT enantiomers.