In the upcoming field of DNA nano-science, DNA is used as an entity for building higher order self-assembled structures rather than for storage of genetic information. The application of DNA as a building block relies, like its biological blueprinting function, on the specific pairing between bases holding pairs of DNA molecules together. However, the complexity involved in building even simple DNA architectures is usually so high that designing structures from more than a few base sequences makes the use of computer programs indispensible. Moreover, synthetic DNA nano-structures are often time-consuming and expensive to build and their structures can be difficult to validate. Therefore, atomistic simulations, which can predict assembly efficiency and physical properties of the designed structures are of great value for both the processes of design and characterization. In this article we summarize examples of computational tools for the design and characterization of DNA nano-structures with particular emphasis on a three-dimensional truncated octahedral structure.