Name: analyzing and building nucleic acid structures with 3dna
Uploaded: 2013-04-26T12:00:00
Description: Watch this Scientific Journal Video about Analyzing and Building Nucleic Acid Structures with 3DNA at JoVE.com

We are grateful to Ji&#345;&iacute; &Scaron;poner for sharing the coordinates of DNA double helices generated in molecular dynamics simulations. We also acknowledge Nada Spackova for assistance in downloading these structures. Support of this work through USPHS Research Grants GM34809 and GM096889 is gratefully acknowledged.

1. Installation of the Software Package
<ol>
	<li>Connect to the 3DNA website at <a href="http://x3dna.org" target="_blank">http://x3dna.org</a> and click the link to the 3DNA Forum. Within the Forum select the 'register' link and follow the instructions to create a new account.</li>
	<li>The following instructions detail installation of the software on an OS X-based Macintosh computer with a default 'bash' shell. The procedure for Linux or Windows (Cygwin, MinGW/MSYS) systems with commonly used shells (including 'tcsh...

<ol>
	<li>Lu, X. -. J., Olson, W. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3DNA:+a+software+package+for+the+analysis,+rebuilding,+and+visualization+of+three-dimensional+nucleic+acid+structures.">3DNA: a software package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures.</a> Nucleic Acids Res. 31, 5108-5121 (2003).</li><li>Lu, X. -. J., Olson, W. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3DNA:+a+versatile,+integrated+software+system+for+the+analysis,+rebuilding,+and+visualization+of+three-dimensional+nucleic-acid+structures.">3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures.</a> Nature Protocols. 3, 1213-1227 (2008).</li><li>Zheng, G., Lu, X. -. J., Olson, W. 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K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3DNALandscapes:+a+database+for+exploring+the+conformational+features+of+DNA.">3DNALandscapes: a database for exploring the conformational features of DNA.</a> Nucleic Acids Res. 38, 267-274 (2010).</li><li>Tolstorukov, M. Y., Colasanti, A. V., McCandlish, D., Olson, W. K., Zhurkin, V. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+'roll-and-slide'+mechanism+of+DNA+folding+in+chromatin.+Implications+for+nucleosome+positioning.">A novel 'roll-and-slide' mechanism of DNA folding in chromatin. Implications for nucleosome positioning.</a> J. Mol. Biol. 371, 725-738 (2007).</li><li>Lu, X. -. J., Olson, W. K., Bussemaker, H. 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The set of protocols presented in this article only touch upon the capabilities of the 3DNA suite of programs. The tools can be applied to RNA structures to identify non-canonical base pairs, to determine the secondary structural contexts in which such pairing occurs, to quantify the spatial disposition of helical fragments, to measure the overlap of bases along the chain backbone, etc. The rebuild command allows the user to construct simple and informative block representations of the bases and base pairs like that show...

Understanding the three-dimensional structures of DNA, RNA, and their complexes with proteins, drugs, and other ligands, is crucial for deciphering their diverse biological functions, and for allowing the rational design of therapeutics. Exploration of such structures entails three separate, yet closely related components: analysis (to extract patterns in shapes and interactions), modeling (to assess energetics and molecular dynamics), and visualization. Structural analysis and model building are essentially two sides of the same coin, and visualization complements both of them.
The 3DNA suite of computer programs is an increasingly popular structural bioinformatics toolkit with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. Earlier publications outlined the capabilities of the software1, provided recipes to perform selected tasks2, introduced the web-based interface to popular features of the software3, presented databases of structural features collected using 3DNA4, 5 and illustrated the utility of the software in the analysis of both DNA and RNA structures6, 7.
The goal of this article is to bring the 3DNA software kit to laboratory scientists and others with interests and/or needs to investigate DNA and RNA spatial organization with state-of-the-art computational tools. The protocols presented here include step-by-step instructions (i) to download and install the software on a Mac OS X system, (ii-iii) to analyze and modify DNA structures at the level of the constituent base-pair steps, (iv-v) to analyze and align sets of related DNA structures, and (vi) to construct models of protein-decorated DNA chains with the user-friendly w3DNA web interface. The software has the capability to analyze individual structures solved using X-ray crystallographic methods as well as large ensembles of structures determined with nuclear magnetic resonance (NMR) methods or generated by computer-simulation techniques.
The structures examined here include (i) the high-resolution crystal structure of DNA bound to the Hbb protein from Borrelia burgdorferi8 (the tick-borne bacterium that causes Lyme disease in humans9, 10), (ii) two large sets of sequentially related DNA molecules produced with molecular simulations11 - 4,500 snapshots of d(GGCAAAATTTTGCC)2 and d(CCGTTTTAAAACGG)2 collected at 100-psec increments during the calculations, and (iii) a small ensemble of NMR-based structures of the O3 DNA operator bound to the headpieces of the Escherichia coli Lac repressor protein12. The instructions below include information on how to access the files of atomic coordinates associated with each of these structures as well as how to use 3DNA (a copy of this file is found on the 3DNA forum at <a href="http://forum.x3dna.org/jove" target="_blank">http://forum.x3dna.org/jove</a>) to examine and modify these structures.

analyzing and building nucleic acid structures with 3dna

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 <a href="http://w3dna.rutgers.edu" target="_blank">http://w3dna.rutgers.edu</a>, 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.

The 3DNA software tools are routinely used to analyze nucleic acid structures. For example, the identities of base pairs and the rigid-body parameters that characterize the arrangements of bases in double-helical fragments of DNA and RNA structures are automatically computed and stored for each new entry in the Nucleic Acid Database22, a worldwide repository of nucleic acid structural information. The values of the rigid-body parameters determined with Protocol 2 readily reveal distortions in three-dimensional...

Watch this Scientific Journal Video about Analyzing and Building Nucleic Acid Structures with 3DNA at JoVE.com

Analyzing and Building Nucleic Acid Structures with 3DNA

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.

The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic ...

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