Rapid prototyping of 3D DNA-origami shapes with caDNAno

TLDR

DNA nanotechnology uses base‑pairing specificity to create custom‑shaped, self‑assembling macromolecular objects, but designing these structures is often cumbersome and time‑consuming. The authors present caDNAno, an open‑source GUI tool that streamlines the design of 3D DNA‑origami honeycomb‑pleated shapes built on scaffolded DNA origami. The approach employs a long scaffold strand to template hundreds of staple strands into cross‑linked helices, adapted to produce 3D honeycomb‑pleated double‑helix layers, and caDNAno facilitates sequence design with example designs and tutorials available online. Using caDNAno markedly reduces the effort required to design 3D DNA‑origami structures. The source code is released under the MIT license.

Abstract

DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures, a long 'scaffold' strand can be employed to template the assembly of hundreds of oligonucleotide 'staple' strands into a planar antiparallel array of cross-linked helices. We recently adapted this 'scaffolded DNA origami' method to producing 3D shapes formed as pleated layers of double helices constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here we present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3D honeycomb-pleated shapes A series of rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3D DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.