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

Nature Protocols volume 3, pages 1213–1227 (2008)Cite this article

Abstract

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 http://3dna.rutgers.edu/.

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Figure 1: Pictorial definitions of rigid-body parameters used to describe the geometry of complementary (or noncomplementary) base pairs and sequential base-pair steps.
Figure 2: Schematic diagrams of three representative rigid-body parameters.
Figure 3: 3DNA-generated images of 22-bp DNA duplexes with the same overall 45° curvature per helical turn.
Figure 4: Images of a B–Z-junction structure63.
Figure 5: 3DNA-generated view of a four-way DNA–RNA junction64 (PDB entry 1EGK), highlighting, with cylinders, the two straight helical regions detected by the program and orienting the structure into a view perpendicular to the long axes of the cylinders.
Figure 6: Two pentaplets from the refined crystal structure of the H. marismortui large ribosomal subunit65 (PDB entry 1JJ2) automatically detected and illustrated with 3DNA.
Figure 7: Schematic nmr_ensemble-generated images of the bases and backbones of the 3′-UTR Y-stem from the poliovirus RNA genome70.
Figure 8: DNA hydration patterns automatically extracted and illustrated with 3DNA from the currently best-resolved nucleosome core-particle structure71.

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Acknowledgements

This work has been generously supported by the U.S. Public Health Service under research grant GM20861. We are grateful to Mauricio Esguerra and Guohui Zheng for their careful reading of the manuscript and independent validation of the protocols presented in this manuscript and to the users of 3DNA for using the software to address real-world problems, and communicating the difficulties that they encounter. Positive interactions with the users have been the driving force behind the development and improvement of 3DNA. We also thank the editor and the anonymous reviewers whose comments helped to clarify the presentation of the protocols.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers—The State University of New Jersey, Piscataway, 08854-8087, New Jersey, USA

    Xiang-Jun Lu & Wilma K Olson

  2. Department of Biological Sciences and Center for Computational Biology and Bioinformatics, Columbia University, New York, 10027, New York, USA

    Xiang-Jun Lu

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  1. Xiang-Jun Lu
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Correspondence to Xiang-Jun Lu or Wilma K Olson.

Supplementary information

Supplementary Data

Rectangular base-pair block of size (4.5-by-10-by-0.5) in Alchemy format (ZIP 0 kb)

Supplementary Data

Input file for "rebuild" of 45-degree propeller used in Recipe#1, Box 3 (ZIP 0 kb)

Supplementary Data

Input file for "rebuild" of roll-introduced DNA curvature used in Recipe#2, Box 3. This file uses a short-handed form with only 6 dimer step parameters, explicitly setting the six base-pair parameters (propeller, buckle etc) to zeros. (ZIP 0 kb)

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Lu, XJ., Olson, W. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc 3, 1213–1227 (2008). https://doi.org/10.1038/nprot.2008.104

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