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A comprehensive software package for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. 3DNA can be applied to parallel and antiparallel double helices, single-stranded forms, multi-stranded helices and complex tertiary folding motifs found in both DNA and RNA structures. The rebuilding module of 3DNA can be used to generate sequence-dependent atomic structures of nucleic acids, with or without the sugar–phosphate backbone. These structures provide a useful starting point for molecular mechanics and molecular dynamics calculations.

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3DNA classification

3DNA specifications

Software type:
Restrictions to use:
Computer skills:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows

3DNA distribution


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3DNA support



  • Xiang-Jun Lu <>

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Department of Chemistry and Chemical Biology, Wright-Rieman Laboratories, The State University of New Jersey, Piscataway, NJ, USA

Funding source(s)

This work has been supported by the US Public Health Service under research grant GM20861.

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