• Molecular Canvas

    1. Dimensions:

      • Height: Units of DNA Helices
      • Width: Units of DNA Helices
      • Depth: Units of DNA base pairs (multiples of 8)

    2. Navigation Panel:

      The navigation panel on the left can be used to translate, rotate and zoom in/out of the molecular canvas. After naming the project and entering the dimensions, a new project is created at ~/Desktop/3DNA_Workspace The molecular canvas can also be navigated using mouse:
      • Translate: Right Button press + mouse movement
      • Rotate: Left Button press + mouse movement
      • Zoom: Mouse scroll press + mouse Up movement (Zoom In)/mouse Down movement (Zoom Out)

    3. 3DNA console:

      All the actions performed on the molecular canvas can be tracked as on screen events on the user console situated on the bottom side of the software.

    4. Advanced options:

      Advanced options pertaining to molecular sculpting can be accessed by clicking on the icon on the top bar These include:
        Delete multiple voxels:
        1. Delete Plane
        2. Delete Row/Column
        Choosing DNA sequences list :
        1. Random Sequences
        2. Import Sequences
        Other options:
        1. Toggling boundary bricks
        2. Toggling protector bricks
        3. Enabling crystal options

  • Sculpting the Canvas

    1. Removing indivdual voxels:

      To remove voxels one at a time using mouse, click on it to deselect it from the canvas. To undo voxel deselection click on the undo icon present in the navigation bar.

    2. Multiple voxel delete:

      To remove multiple voxels (row/columns/planes) use deleting options from the advanced panel

  • Sculpting the Canvas

    1. Removing indivdual voxels:

      To remove voxels one at a time using mouse, click on it to deselect it from the canvas. To undo voxel deselection click on the undo icon present in the navigation bar.

    2. Multiple voxel delete:

      To remove multiple voxels (row/columns/planes) use deleting options from the advanced panel

  • 3DNA advanced options

    1. Protector bricks:

      Protector bricks are half poly-1T domains which prevent unwanted hybridization of DNA strands at the front and the back faces (along the z-axis) of the 3D structure.

    2. Boundary bricks:

      These are 48 nucleotide bricks formed by the concatenation of short 16 nucleotide bricks with longer 32 nucleotide bricks on the boundary surface of the structure.

    3. Crystal:

      A crystal is a continuous DNA brick structure formed by the hybridization of similar building blocks of smaller size. Compatibility of planes at the front and back faces based on the orientation of DNA bricks is as follows:
      Front -> Back
      • North -> West
      • West -> South
      • South -> East
      • East -> North

  • 3DNA saving and visualization

    1. Saving:

      After designing the prescribed structure, the final data can be saved using the random DNA sequence generator or by importing a fixed set of DNA sequences
      • Random sequences: These are the sequences provided by the random sequence generator
      • Import sequences: User can also import their own set of DNA sequences for envisaging shapes. The sequences must be imported as 3 separate .csv files with a fixed syntax. For further details on the syntax refer 3DNA user manual.

    2. Visualization:

      Once the voxels have been mapped to DNA sequences, the underlying DNA brick structure can be visualized. Visualization options:
      • Elementary Visualization
      • Full canvas Visualization
      • Individual plane Visualization

For comments and feedback, contact us by email: 3dna [at] guptalab.org

3DNA 2.0 has been developed by Foram Joshi and Shikhar K Gupta under the supervision of Dr. Manish K. Gupta in collabration with Dr. David M. Smith at
DNA Nanodevices Unit, Fraunhofer IZI, Leipzig, Germany. 3DNA (copyright © 2014 Dr.Manish K. Gupta) has been developed by Foram Joshi and Shikhar K Gupta with contributions from Dixita Limbachiya at
the Laboratory of Natural Information Processing (Group of Prof. Manish K. Gupta)

Dhirubhai Ambani Institute of Information and Communication Technology
Room 2209 Faculty Block 2, Near Indroda Circle, Gandhinagar, Gujarat INDIA 382 007
Phone: 91-79-30510549, Fax: 91-79-30520010. Phone: 91-79-30510552.
Any selling or distribution of the program or its parts, original or modified, is prohibited without a written permission from Manish K. Gupta. Last updated on Feb 14, 2014.