CanDo - Computer-aided Engineering for DNA origami

CanDo - Computer-aided Engineering for DNA origami

Scaffolded DNA origami enables the programmable synthesis of complex DNA-based nanostructures with a broad range of potential scientific and industrial applications [1-6]. DNA origami entails folding a multiple kilobase single-stranded ‘scaffold’ DNA molecule into a custom shape using a set of shorter, single-stranded ‘staple’ oligonucleotides. The effective design of complex DNA origami shapes promises to benefit greatly from computational prediction of the expected solution shape and mechanical properties of conceptual designs prior to initiating cost-intensive staple oligonucleotide synthesis. Computational feedback is particularly useful in the design of sophisticated multi-layer structures that include curved or twisted elements [4]. With this online resource we offer to designers of DNA origami the computational prediction of single- and multi-layer DNA origami structures, including their mean deformed 3D conformation and conformational flexibility. Analysis is performed using a finite-element-based modeling framework for DNA with single base-pair resolution, with input provided by design files created using caDNAno [5] on a honeycomb [2] or square lattice [4]. The utility of the framework is illustrated on the Examples & Applications page of this website, where several sophisticated linear and non-linear structures including curvature and twist are predicted. Practical information on how to approach the design and production of DNA origami shapes can be found at DNA-origami.org and in the following primer on scaffolded DNA origami [6].