Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures - PubMed (original) (raw)

. 2009 Jul;37(Web Server issue):W240-6.

doi: 10.1093/nar/gkp358. Epub 2009 May 27.

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Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

Guohui Zheng et al. Nucleic Acids Res. 2009 Jul.

Abstract

The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their complexes with proteins and other ligands. The server allows the user to determine a wide variety of conformational parameters in a given structure--such as the identities and rigid-body parameters of interacting nucleic-acid bases and base-pair steps, the nucleotides comprising helical fragments, etc. It is also possible to build 3D models of arbitrary nucleotide sequences and helical types, customized single-stranded and double-helical structures with user-defined base-pair parameters and sequences, and models of DNA 'decorated' at user-defined sites with proteins and other molecules. The visualization component offers unique, publication-quality representations of nucleic-acid structures, such as 'block' images of bases and base pairs and stacking diagrams of interacting nucleotides. The w3DNA web server, located at http://w3dna.rutgers.edu, is free and open to all users with no login requirement.

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Figures

Figure 1.

Figure 1.

Screenshots illustrating the information provided in the analysis of nucleic-acid-containing structures with valid Protein Data Bank identifiers (PDB ID), here the ensemble of 20 structures of the complex of DNA with the human TTAGGG-repeat binding factor TRF1 determined by multidimensional heteronuclear NMR spectroscopy (18) (PDB ID: 1IV6). The output comprises, but is not limited to: (a) a brief description of the structural file, including the author(s), compound(s), number of models, external links, etc., (b) a gallery of block representations of each model in the file, which by moving the mouse over the icons, reveals the fluctuations in the structural ensemble and by clicking a specific icon, points to the set of parameters describing the chosen model, (c) a summary file with a comprehensive list of structural parameters, which can be viewed or downloaded by clicking the appropriate icons, (d) tables of selected parameters, which can be displayed by clicking on one of the links and sorted by clicking on the headers of the columns in the selected table, (e) the page, redirected from (a) via the ‘Analyze multiple models’ button, with links to the summary files for all of the models of the protein–DNA complex.

Figure 2.

Figure 2.

Representations of nucleic-acid-containing structures generated with the reconstruction component of the w3DNA server. (a) Two 100 nucleotide strands of poly(rU) complexed with the same length of poly(rA) in the classic 11-fold RNA poly(rU)·poly(rA)·poly(rU) triple helical structure (19,20) (3DNA fiber model 32). (b) A 100 base-pair curved DNA block copolymer made up respectively of A-, B-, and C-form double-helical fragments (19,20) (3DNA fiber models 1, 4, and 7) of G35·C35, A35·T35, and (GA)15·(TC)15. (c) A 210 base-pair B-form DNA ‘decorated’ with 4 HU proteins. The protein-bound steps—centered at base pairs 41, 89, 137, and 185—are assigned the sequence and rigid-body parameters of the central 17 base pairs in the 1.90-Å crystal complex with Anabaena HU (29) (PDB ID: 1P71). The protein-free DNA steps are fixed in the canonical B form and assigned a homopolymeric repeating sequence (An·Tn), where n is respectively 31, 28, 28, 28, and 16 base pairs. Color-coded tubes on RNA and DNA trace the progression of the backbone defined by the phosphorus atoms: strand I (red); strand II (yellow); strand III (green). Color coding of nucleotide sequence conforms to the Nucleic Acid Database standard (9): A (red); C (yellow); G (green); T (blue). Violet ribbons connecting protein Cα carbons generated with MolScript (

http://www.avatar.se/molscript/

).

Figure 3.

Figure 3.

Examples of the unique representations of nucleic-acid structures available through the w3DNA server. (a) Color-coded composite block/backbone/tube representation of the DNA in the currently best-resolved nucleosome core-particle structure (31) (PDB ID: 1KX5). (b) Stacking diagram illustrating the overlap and hydrogen-bonding patterns of adjacent base pairs (C19·G49 and U20·A48) in model 1 from the ensemble of NMR structures of the complex of a 55 nucleotide fragment of X. laevis 5S rRNA with three zinc fingers of transcription factor TFIIIA (32) (PDB ID: 2HGH). (c) Schematic ‘NMR-ensemble’ image of the bases, RNA backbones, and protein ribbons in 15 of the 20 models of the aforementioned RNA–protein complex (32). Color coding identical to that in Figure 2, save for the depiction of U in aqua.

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