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.

The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the f luctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequencespecific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as f lexible ''hinges'' fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic threedimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.In addition to the genetic message, DNA base sequence carries a multitude of other signals related to the manipulation of the long, thread-like molecule. Primary sequences of nucleic acid bases determine three-dimensional structures whose physical properties reflect the constituent residues. The existing library of solved DNA crystal structures (1), for example, reveals subtle sequence-dependent irregularities in the orientation and displacement of adjacent residues (2). Duplex stability under a given set of environmental conditions also depends to good approximation on the identity of the 10 nearest neighbor base pairs (3). The linear sequence of genetic information thus expands into a base sequence-dependent spatial and energetic code that governs the global organization of the double helix and its susceptibility to interactions with other molecules.Interest in understanding the physical properties of genomic DNA has prompted the development of new approaches to analyze and depict the sequence-dependent bending and twisting of neighboring base pairs. Studies of gel migration (4), chain cyclization kinetics (4, 5), and nucleosome phasing (6) have yielded a variety of sequence-dependent models to account for the observed data. Furthermore, collected oligonucleotide crystal structures show similar conformational trends (2), although there are discrepancies between the x-ray and solution assessments of the direction of bending at a few dimer steps (7,8). The solid state data additionally reveal sequence-dependent differences in the displacement of base pairs [see, e.g., Slide (2)], a ...

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, etc. 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/.