DNA origami is a technique used to build bio-compatible structures at the nanometer scale with remarkable ease and precision. The technique consists in letting self-assemble a carefully designed network of DNA strands.
The key step in DNA origami design is the positioning of crossovers, which constrains the structure geometrically to adopt the desired shape. This important task is made difficult by the peculiar geometry of the DNA double helix. Software and empirical patterns have been proposed to assist the designer, yielding to increasingly complex structures. However, the limited precision of these rules forces the DNA origami design to involve several passes of validation using simulation software, as well as several experimental trials of assembly and characterizations (by atomic force or electron microscopy) before obtaining the desired shape with a satisfying precision and yield.
In this work, we lead a reflection on what constitutes a good user software for designing DNA origami. We develop a model of DNA nanostructures that is simple enough to be manipulated through intuitive interfaces, without compromising on precision and fine tuning. We also develop a new geometrical model for curved DNA helices allowing a new nature-inspired spiral-based method for routing helices along curved surfaces. We implement all these new methods in our new software, ENSnano.
Our geometric approach allows crossover locations to be directly deduced from the intended geometry of the desired shape. We provide experimental evidence of their efficiency by designing and accurately assembling origami with unprecedentedly complex 3D curvatures.