The CanDo (.cndo) file format, which was designed to describe DNA nanostructures, contains sufficient information to generate the all-atom models of these DNA nanostructures. This atomic model generator stores four standard reference atomic structures of basepairs A-T, T-A, G-C, and C-G. Each standard reference atomic structure consists of two phosphates, two deoxyriboses, and two paired bases.  An all-atom model is created by placing the standard reference atomic structures, using rigid-body translation and rotation, to the positions and orientations of the basepairs given by the .cndo file format. We have developed a software that generates atomic models from .cndo files. The script is available here.

Users of this tool are kindly requested to cite the following reference:

  • K Pan, DN Kim, F Zhang, MR Adendorff, H Yan, M Bathe. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nature Communications, 5: 5578 (2014). [ Pubmed Article ]

Notes.

  1. This atomic model generator requires MATLAB and UCSF Chimera.
  2. This atomic model generator does not consider conformational change of basepairs, sugars, and phosphates. Users may run the energy minimization script, molecular dynamics simulations, or other computations to simulate atomic-level details of DNA nanostructures.
Here we use the file example_4way_junction.cndo, to demonstrate the use of this atomic model generator. The following steps are run in MATLAB.

Step 1. Add the two directories in the downloaded ZIP package to the MATLAB paths.

>> addpath cndo2atomic_v3.4

>> addpath topology2pdb_ver3_bulge

Step 2. Assign colors for the DNA strands. In this example, if a strand contains less than 100 nucleotides, then a color with the RGB value (190, 190, 190) is assigned to this strand. Otherwise a color with the RGB value (204, 121, 167) is assigned.

>> param.StrandColor = [190 190 190; 86 180, 233];

>> param.L_thres = 100;

Step 3. Assign the rendering resolution (typically between 3 and 6) and figure size (typically 640-by-480).

>> param.molmapResolution = 3;

>> param.WindowSize = [640 480];

Step 4. Assign the path to UCSF Chimera.

>> param.chimeraEXE = ‘”C:\Program Files\Chimera 1.8\bin\chimera.exe”‘;

>> param.chimeraOPTION = ‘––silent ––script’;

Step 5. Generate the atomic model

>> CAD_path = ‘example_4way_junction.cndo’;

>> work_DIR = ‘example_4way_junction’;

>> main_cndo2pdb(CAD_path, work_DIR, param);

Finally, a directory ‘example_4way_junction’ is created in the current working directory. The files in the directory ‘example_4way_junction’ should be the same as those in example_4way_junction.zip. The generated atomic structure is shown below.

Fig_WP-5-2_1

The design of the DNA tetrahedron is in tetrahedron.cndo. Repeats steps 1-4 in Example 1. In step 5, enter

>> CAD_path = ‘tetrahedron.cndo’;

>> work_DIR = ‘tetrahedron’;

>> main_cndo2pdb(CAD_path, work_DIR, param);

A directory ‘tetrahedron’ is created in the current directory and is available here. The generated atomic structure is shown below.

tetrahedron

The design of the DNA icosahedron is in icosahedron.cndo. Repeats steps 1-4 in Example 1. In step 5, enter

>> CAD_path = ‘icosahedron.cndo’;

>> work_DIR = ‘icosahedron’;

>> main_cndo2pdb(CAD_path, work_DIR, param);

A directory ‘icosahedron’ is created in the current directory and is available here. The generated atomic structure is shown below.

icosahedron_y90

The design of the DNA four-layer ring is in 4_layer.cndo. Repeats steps 1-4 in Example 1. In step 5, enter

>> CAD_path = ‘4_layer.cndo’;

>> work_DIR = ‘4_layer’;

>> main_cndo2pdb(CAD_path, work_DIR, param);

A directory ‘4_layer’ is created in the current directory and is available here. The generated atomic structure is shown below.

4_layer_x90

The design of the DNA hemisphere is in hemisphere.cndo. Repeats steps 1-4 in Example 1. In step 5, enter

>> CAD_path = ‘hemisphere.cndo’;

>> work_DIR = ‘hemisphere’;

>> main_cndo2pdb(CAD_path, work_DIR, param);

A directory ‘hemisphere’ is created in the current directory and is available here. The generated atomic structure is shown below.

hemisphere