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Nucleic Acids Res. 2009 Aug;37(15):5001-6. doi: 10.1093/nar/gkp436. Epub 2009 Jun 16.

Rapid prototyping of 3D DNA-origami shapes with caDNAno.

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  • 1Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.


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, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.

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