Stability of DNA-linked nanoparticle crystals I: Effect of linker sequence and length

Abstract

The creation of three-dimensional, crystalline-ordered nanoparticle (NP) structures linked by DNA has proved experimentally challenging. Here we aim to systematically study parameters that influence the relative thermodynamic and kinetic stability of such crystals. To avoid experimental bottlenecks and directly control molecular-scale parameters, we carry out molecular dynamics simulations of a coarse-grained model in which short DNA strands (6 to 12 bp) are tethered to a NP core. We examine the influence of the number of bases per strand L, number of linking bases and the number of spacer bases s on the stability of crystal states. We also consider the effect of using a single linking NP type versus a binary linking system. We explicitly compute the free energy, entropy, and melting point T_M for BCC and FCC lattices. We show that binary systems are preferable for generating BCC lattices, while a single NP type generates the most stable FCC crystals. We propose a simple model for short DNA strands that can account for T_M of all our data. The model also indicates that the heat of fusion between crystal and amorphous phases grows linearly with , providing a route to maximize the relative crystal stability.