Nucleic Acids Research

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Nucleic Acids Research, 2003, Vol. 31, No. 17 5108-5121
© 2003 Oxford University Press

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

Xiang-Jun Lu and Wilma K. Olson^*

Department of Chemistry and Chemical Biology, Wright-Rieman Laboratories, Rutgers–The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA

*To whom correspondence should be addressed. Tel: +1 732 445 3993; Fax: +1 732 445 5958; Email: olson{at}rutchem.rutgers.edu
Present address:
Xiang-Jun Lu, Science Applications International Corporation, Frederick, MD 21702, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar–phosphate backbone and publication quality ‘standardized’ base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.

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