SI2:SSE: Collaborative Research: Integrated Tools for DNA Nanostructure Design and Simulation

While the robustness of the DNA origami method has enabled researchers to fabricate a large diversity of shapes, many design choices are made according to ad hoc rules and heuristics derived from limited empirical data. It would be beneficial to establish a quantitative physical basis for favoring one strand routing over another for a given shape. We have developed Cadnano Toolkit (CTK) and Molecular Dynamics Simulations of Self-Assembled DNA Nanostructures (MrDNA), a suite of programs to augment several aspects of the DNA origami design process.