3DNA logo A Software Package for the Analysis, Rebuilding, and Visualization of Three-dimensional Nucleic Acid Structures
Xiang-Jun Lu & Wilma K. Olson

3DNA was created in the hope that it will be useful, but without any guarantees. Nothing is perfect, and we strive to improve its functionalities. Any comments, constructive suggestions, and bug reports are welcome.

Analysis   [Back to Top]

Using a high-resolution B-DNA dodecamer, bdl084 (Shui et al. (1998), Biochemistry, 37, pp. 8341-8355), as an example, the input and output files for the analysis program (analyze) are as follows:

  • Input
    1. bdl084.pdb: structure file in PDB format downloaded from the NDB/PDB
    2. bdl084.inp: input file describing base-pairing patterns in the original PDB file, generated as follows: find_pair -t bdl084.pdb bdl084.inp
  • Output (generated with: analyze bdl084.inp)
    1. bdl084.out: detailed listing of various parameters
    2. auxiliary.par: auxiliary parameters including phosphorus-phosphorus distance matrix, etc. Fixed file name: overwritten each time unless changed to a new name
    3. bp_helical.par: base-pair and helical parameters (x-displacement, etc.) in a format suitable for rebuilding routines (e.g., rebuild)
    4. bp_step.par: base-pair and step parameters (Roll, Slide etc.) in a format suitable for rebuilding routines
    5. cf_7methods.par: parameters of the seven most frequently used nucleic acid analysis programs-CEHS, CompDNA, Curves, FreeHelix, NGEOM, NUPARM, RNA-calculated based on the standard reference frame. Note that the numerical values are very similar
    6. ref_frames.dat: position and orientation of each base-pair reference frame, useful for re-orienting the structure with frame_mol
    7. poc_haxis.r3d: global linear helical axis with average radii of P, O4' and C1' atoms for input to Raster3D.
    8. hstacking.pdb: multiple structures in PDB format composed of each dinucleotide step with reference to its middle helical frame
    9. stacking.pdb: multiple structures in PDB format composed of each dinucleotide step with reference to its middle step frame. Used for generating "standardized" stacking diagrams

Rebuilding   [Back to Top]

With 3DNA, nucleic acid structures can be generated based on base-pair step and helical parameters as generated by analyze shown above, arbitrary user-defined parameter sets, or regular fiber models.

  • Rebuild based on structural parameters
    1. Illustration of base-pair parameters (download this image in PostScript format)

      Base-pair parameters

    2. A complete helical turn of DNA having Twist = 36°, showing the effects of introducing uniform Roll and Slide at each step. [Calladine & Drew (1997), "Understanding DNA: The Molecule and How It Works", 2nd Edition, pp56.]

      Regular DNA (A-, and B-form)

    3. Two complete helical turns of DNA, with a curvature of 45° per turn, or 4.5° per step on average. Such tight curvature may be achieved, in principle, by any of the distributions of Roll angle shown in parts (a) to (d). [Calladine & Drew (1997), "Understanding DNA: The Molecule and How It Works", 2nd Edition, pp78.]

      Roll induced DNA bending

  • Fiber models: 55 fiber models can be conveniently generated with the program fiber.

Visualization   [Back to Top]

  • Stacking diagrams: based on the file stacking.pdb generated with analyze shown above, the following image can be produced directly with stack2img and rendered with Raster3D.

    stacking diagram

  • Base multiplets can be automatically identified and oriented in the best view with the utility program find_pair. The following image was generated with r3d_atom and rendered with Raster3D.

    base multiplet

  • Double helical regions are automatically identified by find_pair, and relatively straight helices can be rendered as cylinders, as shown in the following example of a nucleic acid junction (Nowakowski et al. (2000) J Mol Biol., 300(1), pp.:93-102).

    DNA junction

  • The schematic output from 3DNA progams, such as stack2img, r3d_atom and blocview, can also be fed directly to PyMol to get high-quality ray-traced images, as shown in the following examples:

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