Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

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/.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

References

  1. Tolstorukov, M.Y., Colasanti, A.V., McCandlish, D., Olson, W.K. & Zhurkin, V.B. A novel 'roll-and-slide' mechanism of DNA folding in chromatin. Implications for nucleosome positioning. J. Mol. Biol. 371, 725–738 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Luscombe, N.M., Laskowski, R.A. & Thornton, J.M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29, 2860–2874 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lu, X.-J., Shakked, Z. & Olson, W.K. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300, 819–840 (2000).

    Article  CAS  PubMed  Google Scholar 

  4. Tinoco, I. Jr. & Bustamante, C. How RNA folds. J. Mol. Biol. 293, 271–281 (1999).

    Article  CAS  PubMed  Google Scholar 

  5. Auffinger, P. & Westhof, E. Rules governing the orientation of the 2′-hydroxyl group in RNA. J. Mol. Biol. 274, 54–63 (1997).

    Article  CAS  PubMed  Google Scholar 

  6. Leontis, N.B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dickerson, R.E. et al. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 208, 787–791 (1989).

    Google Scholar 

  8. Lu, X.-J. & Olson, W.K. Resolving the discrepancies among nucleic acid conformational analyses. J. Mol. Biol. 285, 1563–1575 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Olson, W.K., Gorin, A.A., Lu, X.-J., Hock, L.M. & Zhurkin, V.B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA 95, 11163–11168 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Olson, W.K., Colasanti, A.V., Lu, X.-J. & Zhurkin, V.B. Physico-chemical properties of nucleic acids: character and recognition of Watson-Crick base pairs. In Wiley Encyclopedia of Chemical Biology. 10.1002/9780470048672.wecb452 (John Wiley & Sons, Hoboken, NJ, USA, 2008).

    Google Scholar 

  11. Olson, W.K. et al. A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 313, 229–237 (2001).

    Article  CAS  PubMed  Google Scholar 

  12. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Ångstrom resolution. Science 289, 905–920 (2000).

    Article  CAS  PubMed  Google Scholar 

  13. Mandel-Gutfreund, Y., Margalit, H., Jernigan, R.L. & Zhurkin, V.B. A role for C···O interactions in protein–DNA recognition. J. Mol. Biol. 277, 1129–1140 (1998).

    Article  CAS  PubMed  Google Scholar 

  14. Treger, M. & Westhof, E. Statistical analysis of atomic contacts at RNA–protein interfaces. J. Mol. Recognit. 14, 199–214 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Suzuki, M. DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl. Acad. Sci. USA 91, 12357–12363 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Tatano, M. et al. DNA recognition by β-sheets. Biopolymers 44, 335–359 (1997).

    Article  Google Scholar 

  17. Jones, S., van Heyningen, P., Berman, H.M. & Thornton, J.M. Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287, 877–896 (1999).

    Article  CAS  PubMed  Google Scholar 

  18. Nadassy, K., Wodak, S.J. & Janin, J. Structural features of protein-nucleic acid recognition sites. Biochemistry 38, 1999–2017 (1999).

    Article  CAS  PubMed  Google Scholar 

  19. Luscombe, N.M., Laskowski, R.A. & Thornton, J.M. NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res. 25, 4940–4945 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Woda, J., Schneider, B., Patel, K., Mistry, K. & Berman, H.M. An analysis of the relationship between hydration and protein–DNA interactions. Biophys. J. 75, 2170–2177 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kono, H. & Sarai, A. Structure-based prediction of DNA target sites by regulatory proteins. Protein-Struct. Func. Genet. 35, 114–131 (1999).

    Article  CAS  Google Scholar 

  22. Pichierri, F., Aida, M., Gromiha, M.M. & Sarai, A. Free-energy maps of base-amino acid interactions for DNA–protein recognition. J. Am. Chem. Soc. 121, 6152–6157 (1999).

    Article  CAS  Google Scholar 

  23. Ge, W., Schneider, B. & Olson, W.K. Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. Biophys. J. 88, 1166–1190 (2005).

    Article  CAS  PubMed  Google Scholar 

  24. Lu, X.-J. & Olson, W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108–5121 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zhurkin, V.B., Lysov, Y.P. & Ivanov, V.I. Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 6, 1081–1096 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Bolshoy, A., McNamara, P., Harrington, R.E. & Trifonov, E.N. Curved DNA without A–A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88, 2312–2316 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. El Hassan, M.A. & Calladine, C.R. The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme. J. Mol. Biol. 251, 648–664 (1995).

    Article  CAS  PubMed  Google Scholar 

  28. Lu, X.-J., El Hassan, M.A. & Hunter, C.A. Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). J. Mol. Biol. 273, 668–680 (1997).

    Article  CAS  PubMed  Google Scholar 

  29. Lu, X.-J., El Hassan, M.A. & Hunter, C.A. Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J. Mol. Biol. 273, 681–691 (1997).

    Article  CAS  PubMed  Google Scholar 

  30. Lu, X.-J., Babcock, M.S. & Olson, W.K. Mathematical overview of nucleic acid analysis programs. J. Biomol. Struct. Dynam. 16, 833–843 (1999).

    Article  CAS  Google Scholar 

  31. Berman, H.M. et al. The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sühnel, J. Views of RNA on the World Wide Web. Trends in Genetics 13, 206–207 (1997).

    Article  PubMed  Google Scholar 

  33. Merritt, E.A. & Bacon, D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).

    Article  CAS  PubMed  Google Scholar 

  34. Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Auffinger, P. & Hashem, Y. SwS: a solvation web service for nucleic acids. Bioinformatics 23, 1035–1037 (2007).

    Article  CAS  PubMed  Google Scholar 

  36. Dixit, S.B. & Beveridge, D.L. Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. Bioinformatics 22, 1007–1009 (2006).

    Article  CAS  PubMed  Google Scholar 

  37. Dror, O., Nussinov, R. & Wolfson, H. The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res. 34, W412–W415 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. van Dijk, M., van Dijk, A.D.J., Hsu, V., Boelens, R. & Bonvin, A.M.J.J. Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res. 34, 3317–3325 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Banerjee, A. et al. Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor. J. Chem. Inf. Model. 47, 2216–2227 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Babcock, M.S., Pednault, E.P.D. & Olson, W.K. Nucleic acid structure analysis: mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237, 125–156 (1994).

    Article  CAS  PubMed  Google Scholar 

  41. Clowney, L., Jain, S.C., Srinivasan, A.R., Westbrook, J., Olson, W.K. & Berman, H.M. Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118, 509–518 (1996).

    Article  CAS  Google Scholar 

  42. Dickerson, R.E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906–1926 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Gorin, A.A., Zhurkin, V.B. & Olson, W.K. B-DNA twisting correlates with base pair morphology. J. Mol. Biol. 247, 34–48 (1995).

    Article  CAS  PubMed  Google Scholar 

  44. Lavery, R. & Sklenar, H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6, 63–91 (1988).

    Article  CAS  Google Scholar 

  45. Lavery, R. & Sklenar, H. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dynam. 6, 655–667 (1989).

    Article  CAS  Google Scholar 

  46. Macke, T. & Case, D.A. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids (eds. Leontis, N.B. & SantaLucia J. Jr.) 379–393 (American Chemical Society, Washington, DC, 1998).

    Google Scholar 

  47. Tung, C.-S. & Carter, E.S. II Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. Bioinformatics 10, 427–433 (1994).

    Article  CAS  Google Scholar 

  48. Major, F. Building three-dimensional ribonucleic acid structures. IEEE Comput. Sci. Eng. 5, 44–53 (2003).

    Article  CAS  Google Scholar 

  49. Sayle, R.A. & Milnerwhite, E.J. RasMol: biomolecular graphics for all. Trends Biochem. Sci. 20, 374–376 (1995).

    Article  CAS  PubMed  Google Scholar 

  50. Massire, C., Gaspin, C. & Westhof, E. DRAWNA: a program for drawing schematic views of nucleic acids. J. Mol. Graph. 12, 201–206 (1994).

    Article  CAS  PubMed  Google Scholar 

  51. Huang, C.C., Couch, G.S., Pettersen, E.F. & Ferrin, T.E. Chimera: an extensible molecular modeling application constructed using standard components. Pac. Symp. Biocomput. 1, 724 (1996).

    Google Scholar 

  52. Trifonov, E.N. & Sussman, J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816–3820 (1980).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Hagerman, P.J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry 24, 7033–7037 (1985).

    Article  CAS  PubMed  Google Scholar 

  54. Koo, H.-S., Wu, H.-M. & Crothers, D.M. DNA bending at adenine thymine tracts. Nature 308, 501–506 (1986).

    Article  Google Scholar 

  55. Hagerman, P.J. Sequence-directed curvature of DNA. Nature 321, 449–450 (1986).

    Article  CAS  PubMed  Google Scholar 

  56. Ulanovsky, L.E. & Trifonov, E.N. Estimation of wedge components in curved DNA. Nature 326, 720–722 (1987).

    Article  CAS  PubMed  Google Scholar 

  57. Schultz, S.C., Shields, G.C. & Steitz, T.A. Crystal structure of a CAP–DNA complex: the DNA is bent by 90°. Science 253, 1001–1007 (1991).

    Article  CAS  PubMed  Google Scholar 

  58. Parkinson, G., Wilson, C., Gunasekera, Ebright, Y.W., Ebright, R.E. & Berman, H.M. Structure of the CAP–DNA complex at 2.5 Å resolution: a complete picture of the protein–DNA interface. J. Mol. Biol. 260, 395–408 (1996).

    Article  CAS  PubMed  Google Scholar 

  59. Richmond, T.J. & Davey, C.A. The structure of DNA in the nucleosome core. Nature 423, 145–150 (2003).

    Article  CAS  PubMed  Google Scholar 

  60. Calladine, C.R., Drew, H.R., Luisi, B.F. & Travers, A.A. Understanding DNA: the Molecule and How It Works Chapter 4 (Elsevier Academic Press, San Diego, CA, 2004).

    Google Scholar 

  61. Olson, W.K., Srinivasan, A.R., Marky, N.L. & Balaji, V.N. Theoretical probes of DNA conformation examining the B leads to Z conformational transition. Cold Spring Harb. Symp. Quant. Biol. 47, 229–241 (1983).

    Article  PubMed  Google Scholar 

  62. Harvey, S.C. DNA structural dynamics: longitudinal breathing as a possible mechanism for the B->Z transition. Nucleic Acids Res. 11, 4867–4878 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Ha, S.C., Lowenhaupt, K., Rich, A., Kim, Y.-G. & Kim, K.K. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437, 1183–1186 (2005).

    Article  CAS  PubMed  Google Scholar 

  64. Nowakowski, J., Shim, P.J., Stout, C.D. & Joyce, G.F. Alternative conformations of a nucleic acid four-way junction. J. Mol. Biol. 300, 93–102 (2000).

    Article  CAS  PubMed  Google Scholar 

  65. Klein, D.J., Schmeing, T.M., Moore, P.B. & Steitz, T.A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20, 4214–4221 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Matsumoto, A. & Olson, W.K. Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level. Biophys. J. 83, 22–41 (2002).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Chen, S., Vojtechovsky, J., Parkinson, G.N., Ebright, R.H. & Berman, H.M. Indirect readout of DNA sequence at the primary-kink site in the CAP–DNA complex: DNA binding specificity based on energetics of DNA kinking. J. Mol. Biol. 314, 63–74 (2001).

    Article  CAS  PubMed  Google Scholar 

  68. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. USA 98, 4899–4903 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Wimberly, B.T., Guymon, R., McCutcheon, J.P., White, S.W. & Ramakrishnan, V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell 97, 491–502 (1999).

    Article  CAS  PubMed  Google Scholar 

  70. Zoll, J., Tessari, M., Van Kuppeveld, F.J.M., Melchers, W.J.G. & Heus, H.A. Breaking pseudo-twofold symmetry in the poliovirus 3′-UTR Y-stem by restoring Watson–Crick base pairs. RNA 13, 781–792 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Davey, C.A., Sargent, D.F., Luger, K., Mäder, A.W. & Richmond, T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319, 1097–1113 (2002).

    Article  CAS  PubMed  Google Scholar 

  72. Westbrook, J., Ito, N., Nakamura, H., Henrick, K. & Berman, H.M. PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 7, 988–992 (2005).

    Article  Google Scholar 

Download references

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.

Author information

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

Authors
  1. Xiang-Jun Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wilma K Olson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

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)

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2008.104

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing