This paper presents an experimental immersive interface for designing DNAcomponents for application in nanotechnology. While much research has been done on immersive visualization, this is one of the first systems to apply advanced interface techniques to a scientific design problem. This system uses tangible 3D input devices (tongs, a raygun, and a multipurpose handle tool) to create and edit a purely digital representation of DNA. The tangible controllers are associated with functions (not data) while a virtual display is used to render the model. This interface was built in collaboration with a research group investigating the design of DNA tiles. A user study shows that scientists find the immersive interface more satisfying than a 2D interface due to the enhanced understanding gained by directly interacting with molecules in 3D space.