Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures


Analysis Visualization Rebuilding Composite Fiber Mutation

The rebuilding component of Web 3DNA 2.0 allows the user to build: 1) 3D models of customized double-helical and single-stranded structures with base pairs and base-pair/nucleotide steps arranged according to user-supplied rigid-body parameters, 2) a mixed DNA structure comprised of canonical A-, B-, and C-type DNA fragments. The output webpage includes a schematic representation of the constructed model, a PDB-formatted file with full atomic coordinates and a downloadable link, and a 3D interactive visualization of the constructed model.

Example 3-1: Reconstruction of a customized model

Clicking the button directs the user to an interface for building a DNA/RNA model with customized base-pair/nucleotide step parameters.

The user must prepare a file containing the rigid-body parameters for the desired structure. Two example parameter files can be found at the "Test parameters" links. A single click of each button will automatically fill the corresponding content in the text area (one file for double-stranded DNA, the other one for single-stranded RNA). Note that the base-pair step parameters are null for the first base pair, but the parameter of the first base-pair can have non-zero values.

As an alternative, the user can also upload a parameter file in a valid format (please refer to the example parameter files: double-helix DNA and single-stranded RNA).

Next, the user needs to specify whether to construct a full atomic model and to select a sugar type: B-DNA (C2'-endo), A-DNA (C3'-endo), or RNA (C3'-endo). The user can also specify whether to optimize the backbone geometry.

After clicking the “Build Model” button, the user will be directed to a results page shown below.

Example 3-2: Construction of a model that combines of A-, B-, and C-DNA conformational segments

The user can also construct a DNA model with a combination of A, B, and C double-helical components. Clicking the button directs the user to the following interface:

The user then can choose the desired number of segments in the model from a dropdown list (for example "3"). Clicking the "Next" button leads to an intermediate page where the user can select the sequence and conformational form (A-, B-, or C-DNA) of each segment. Note that the input sequence is that of the leading strand.

After clicking the ‘Build’ button, the user will be directed to a results page shown below.