Rapid prototyping of 3D DNA-origami shapes with caDNAno

By Shawn M. Douglas, Adam Henry Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church, William M. Shih. Nucleic Acids Research, 2009

1,160 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/aa8c234d5e205d08d146aa8030685f07f0699de5

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Citations in the corpus

A primer to scaffolded DNA origami (2011, methodology): “Open-source DNA origami design software called caDNAno can facilitate designing DNA origami objects (http://cadnano.org/) 9 .”
Programmable materials and the nature of the DNA bond (2015, methodology): “To address this problem, a number of open-source software packages are now available that aid researchers in developing the strands and sequences required for a particular DNA origami structure (49, 50).”
Universal computing by DNA origami robots in a living animal (2014, neutral): “15) as previously described 19 .”