Probing DNA Based Nanostructures using Molecular Simulations

Recent decades have witnessed the synthesis of many DNA nanostructures with proposed applications in nanotechnology. State of the art molecular dynamics (MD) simulations can be very useful to understand the microscopic structure of these self-assembled structures at nanoscale. We have developed algorithms to build very accurate 3-d atomistic models of various DNA nanostructures like crossover DNA molecules, DNA nanotubes (DNTs) and DNA polyhedra. We investigate the structure, stability and mechanical properties of various DNA nanostructures in salt solution. We find that the persistence length of DNA nanotubes is of the order of micrometer. We have also examined the interaction of DNA nanotubes embeded in the lipid bilayer membranes. We discover that the local rearrangement of lipid molecules can stabilize the DNA nanotubes in the bilayer and DNA backbone modification is not necessary for the partitioning of DNTs in lipid bilayer. The simulation studies on the atomistic model of DNA icosahedron reveal the dynamical behavior of the structure and its interaction with encapsulated cargo. We believe our atomistic studies will give further impetus in the development of structural DNA nanotechnology.