Role of Host Layer Flexibility in DNA Guest Intercalation Revealed by Computer Simulation of Layered Nanomaterials

Abstract

Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg₂Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas−Hérold or a Rüdorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas−Hérold configuration compared to a Rüdorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas−Hérold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas−Hérold structure compared to the Rüdorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.