  Platonic solids such as polyhedra based on DNA have been deployed for
multifarious applications such as RNAi delivery, biological targeting and
bioimaging. All of these applications hinge on the capability of DNA polyhedra
for molecular display with high spatial precision. Therefore high resolution
structural models of such polyhedra are critical to widen their applications in
both materials and biology. Here, we present an atomistic model of a
well-characterized DNA icosahedron, with demonstrated versatile functionalities
in biological systems. We study the structure and dynamics of this DNA
icosahedron using fully atomistic molecular dynamics simulation in explicit
water and ions. The major modes of internal motion have been identified using
principal component analysis. We provide a quantitative estimate of the radius
of gyration (Rg), solvent accessible surface area (SASA) and volume of the
icosahedron which is essential to estimate its maximal cargo carrying capacity.
Importantly, our simulation of gold nanoparticles (AuNP) encapsulated within
DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra
compared to empty icosahedra. This is consistent with experimental results that
show high yields of cargo-encapsulated DNA icosahedra that have led to its
diverse applications for precision targeting. These studies reveal that the
stabilizing interactions between the cargo and the DNA scaffold powerfully
positions DNA polyhedra as targetable nanocapsules for payload delivery. These
insights can be exploited for precise molecular display for diverse biological
applications.
