caDNAno File Submission

This submission page enables the prediction of the 3D equilibrium structure of programmed DNA assemblies that are designed to reside on a honeycomb [3] or square [5] lattice using the drawing program caDNAno [6]. The caDNAno file preparation, input, and CanDo finite element modeling procedure is demonstrated in this tutorial.

Users of this submission link are kindly requested to cite the following references:

  • DN Kim, F Kilchherr, H Dietz, M Bathe. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Research, 40(7):2862-2868 (2012). [ Pubmed Article ]
  • CE Castro, F Kilchherr, DN Kim, EL Shiao, T Wauer, P Wortmann, M Bathe, H Dietz. A primer to scaffolded DNA origami. Nature Methods, 8: 221-229 (2011). [ Pubmed Article ]
User information
DNA geometry Use pre-entered default values or enter your own
DNA mechanical properties Use pre-entered default values or enter your own
Model resolution
caDNAno (.json) file Please exclude all strands from your design that are not used for folding (e.g., staple strands used for polymerization)
Lattice type
Would you like a movie included with your results? Movies for atomic models may take several hours to create.
Would you like the atomic model included with your results? CanDo generates atomic models with up to 10,000 basepairs and atomic movies with up to 1,000 basepairs.
caDNAno (.csv) file for sequence information Please create the caDNAno (.csv) file from the caDNAno (.json) file with caDNAno, and make sure that these two files are consistent. See the CanDo Tutorial for details. Please note that you must check the option 'Fine' under 'Model resolution' to generate an atomic model!