Douglas, Shawn MichaelMarblestone, Adam H.Teerapittayanon, SuratVazquez, AlejandroChurch, GeorgeShih, William2011-02-222009Douglas, Shawn M., Adam H. Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church, and William M. Shih. 2009. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Research 37(15): 5001-5006.0305-1048http://nrs.harvard.edu/urn-3:HUL.InstRepos:4728739DNA 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.en-USJournal Article2011-02-2210.1093/nar/gkp436