Nucleic Acids Research Advance Access originally published online on June 16, 2009
Nucleic Acids Research 2009 37(15):5001-5006; doi:10.1093/nar/gkp436
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Nucleic Acids Research, 2009, Vol. 37, No. 15 5001-5006
© 2009 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited
Chemistry and Synthetic Biology |
Rapid prototyping of 3D DNA-origami shapes with caDNAno
1Department of Cancer Biology, Dana-Farber Cancer Institute, 2Department of Biological Chemistry and Molecular Pharmacology, 3Department of Genetics, Harvard Medical School, Boston, MA 02115, 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138 and 5Department of Physics, Yale University, New Haven, CT 06520, USA
*To whom correspondence should be addressed. Tel: +1 617 632 5143; Fax: +1 617 632 4393; Email: william_shih{at}dfci.harvard.edu
Received February 22, 2009. Revised May 7, 2009. Accepted May 11, 2009.
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.