(Invited) Computational Simulations of Selective Interactions between ssDNA and SWCNTs

Abstract

Structure-specific interactions between single-stranded DNA oligos and SWCNTs form the basis of important selective sorting methods yet remain poorly understood. Among these interactions is the differential affinity of (ATT)4 for one of the two (7,5) enantiomers. To understand the nature of the affinity difference, we have performed molecular dynamics (MD) simulations followed by free energy (replica exchange) calculations over the temperature range of 290 to 727 K. Comparisons between the conformational free energy landscapes of (ATT)4 structure on right-handed and left-handed (7,5) SWCNTs (respectively known as M and P in stereochemical convention) suggest that (ATT)4 has more contact area with M than with the P enantiomer. However, the corresponding end-to-end distances of (ATT)4 fall nearly in the same region on the landscape. Our standard MD simulations for (ATTT)3 interactions with SWCNTs also suggest that this DNA sequence covers (8,4) SWCNT more effectively than (7,6) and (8,3) SWCNTs, which is consistent with our recent dye-quenching experiments.Other experiments have revealed that when guanines in ssDNA oligos are covalently functionalized to SWCNT sidewalls, the extent of functionalization can depend on the position of the guanine within the oligo. Central positions within long oligos (e.g. T15GT15) lead to greater functionalization than end guanine positions (e.g. T30G). We have performed both standard MD and free energy calculations to investigate the source of this effect. For efficient guanine functionalization of SWCNTs, guanine needs to remain adsorbed on the SWCNT surface. Our computational observations suggest that the central guanine within T15GT15 oligo remains adsorbed on the (6,5) SWCNT surface even when the DNA interacts with other neighboring DNA strands. Under these conditions, the end guanine in T30G is destabilized and tends to desorb from (6,5) SWCNT surface due to inter-strand interactions. Our free energy calculations also suggest that oligos with a central guanine assume more elongated DNA conformations at the surface of a (6,5) SWCNT than do oligos with end guanines. We suggest that DNA elongation is associated with more stable adsorption on the SWCNT surface, supporting efficient covalent functionalization of central guanines. Figure 1