Protocol abstract

Nature Protocols 3, 1213 - 1227 (2008)
Published online: 3 July 2008 | doi:10.1038/nprot.2008.104

Subject Categories: Computational and theoretical biology | Spectroscopy and structural analysis

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Xiang-Jun Lu1,2 & Wilma K Olson1

We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases and so on. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar–phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at

  1. Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854-8087, USA.
  2. Department of Biological Sciences and Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10027, USA.

Correspondence to: Xiang-Jun Lu1,2 e-mail:

Correspondence to: Wilma K Olson1 e-mail:


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