A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra

A semiautomatic procedure to build
complex atomistic covalently
linked DNA nanocages has been implemented in a user-friendly, free,
and fast program. As a test set, seven different truncated DNA polyhedra,
composed by B-DNA double helices connected through short single-stranded
linkers, have been generated. The atomistic structures, including
a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular
prism, a pentagonal prism, and a hexagonal prism, have been probed
through classical molecular dynamics and analyzed to evaluate their
structural and dynamical properties and to highlight possible building
faults. The analysis of the simulated trajectories also allows us
to investigate the role of the different geometries in defining nanocages
stability and flexibility. The data indicate that the cages are stable
and that their structural and dynamical parameters measured along
the trajectories are slightly affected by the different geometries.
These results demonstrate that the constraints imposed by the covalent
links induce an almost identical conformational variability independently
of the three-dimensional geometry and that the program presented here
is a reliable and valid tool to engineer DNA nanostructures.