Analyzing and building nucleic acid structures with 3DNA

Andrew V. Colasanti, Xiang Jun Lu, Wilma K. Olson

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

Abstract

The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic acid structure, including the assignment of base pairs and the determination of rigid-body parameters that describe the structure and, in Protocol 3, by a description of the reconstruction of an atomic model of a structure from its rigid-body parameters. The most recent version of 3DNA, version 2.1, has new features for the analysis and manipulation of ensembles of structures, such as those deduced from nuclear magnetic resonance (NMR) measurements and molecular dynamic (MD) simulations; these features are presented in Protocols 4 and 5. In addition to the 3DNA stand-alone software package, the w3DNA web server, located at http://w3dna.rutgers.edu, provides a user-friendly interface to selected features of the software. Protocol 6 demonstrates a novel feature of the site for building models of long DNA molecules decorated with bound proteins at user-specified locations.

Original languageEnglish (US)
JournalJournal of Visualized Experiments
Issue number74
DOIs
StatePublished - Apr 26 2013

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Keywords

  • 3DNA
  • Biochemistry
  • Bioengineering
  • Bioinformatics
  • Biophysics
  • Chemical biology
  • Conformational analysis
  • DNA
  • Genetics
  • Genomics
  • High-resolution structures
  • Issue 74
  • Model building
  • Molecular biology
  • Molecular dynamics
  • Nucleic acid structure
  • Quantitative biology
  • Rna
  • Software
  • Three-dimensional
  • Visualization

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