Under variable experimental conditions, nanoscale supramolecular aggregates of a new class of DNA amphiphile exhibit diverse morphology. Since it is difficult to experimentally characterize the intermolecular interactions in these structures, we employed molecular dynamics simulations to identify two important structural motifs at atomistic resolution and rationalize the importance of annealing in the aggregation pathway. The first of these structural motifs is simply that of the monomeric unit, whose hydrophobic central block was found to favor a cubic conformation, while the DNA and cyanine dye blocks demonstrate greater conformational flexibility. The second of these motifs, termed the "sheet," is composed of monomers stacked in a plane such that the cubic hydrophobic regions are in contact with each other and the hydrophilic blocks shield both faces of the hydrophobic plane from the aqueous solvent. This motif is the hypothesized building block of the two-dimensional nanoscale structure that is in many cases the thermodynamic product. The effects of temperature on the radius of gyration of the DNA blocks within the monomer and the sheet motifs may explain why annealing is crucial to the formation of the thermodynamic product. Overall, our study provides novel insight into and may benefit the future design of robust, biocompatible, and environmentally friendly soft nanomaterials.

Molecular insight into self-assembled DNA amphiphiles from multiscale simulations

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