Molecular simulation study of the assembly of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition

Abstract

DNA functionalisation is a proven route to program an assembly of nanoparticles into a vast array of nanostructures. In this paper, we used coarse-grained molecular dynamics simulations to study DNA-functionalised nanoparticles and demonstrate the effect of grafted DNA strand composition, specifically the placement and number of contiguous G/C bases in the grafted DNA single strands, on the thermodynamics and structure of nanoparticle assembly at varying grafting densities and particle sizes. At a constant G/C content, nanoparticles assemble more readily when the G/C bases are placed on the outer or middle portions of the strands than on the inner portion. In addition, the number of neighbours within the assembled cluster decreases as the placement of the G/C bases goes from the outer to middle to inner sections of the strand. As the G/C content decreases, the cluster dissociation temperature, Td, decreases, as the enthalpic drive to assemble decreases. At a high G/C content (number of grafts and G/C placement are held constant), as particle size decreases, Td increases. This is because the smaller particles experience a lower entropic loss than do larger particles upon assembly. On the other hand, at a low G/C content, small changes in particle size lead to negligible changes in Td.