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

我们非常感谢分享DNA双螺旋分子动力学模拟产生的坐标吉日Šponer的。我们也承认纳达Spackova为协助下载这些结构。通过USPHS研究资助支持这项工作GM34809和GM096889表示感谢。

1。安装软件包<ol><li>连接到的追梦3DNA在<a href="http://x3dna.org" target="_blank">http://x3dna.org</a>网站和单击链接到3DNA论坛。在论坛内，选择“注册”链接，并按照说明进行操作，以创建一个新的帐户。 </li><li>以下说明详细安装一个基于OS X的Macintosh电脑，一个默认的bash&#39;壳上的软件。 Linux或Windows（Cygwin的的MinGW / MSYS）系统常用shell（包括&#39;tcsh的&#39;）的程序内发现3DNA论坛。 </li><li>一旦你已经建立?...

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	<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. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Web+3DNA-a+web+server+for+the+analysis,+reconstruction,+and+visualization+of+three-dimensional+nucleic-acid+structures.">Web 3DNA-a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.</a> Nucleic Acids. Res. 37, W240-W246 (2009).</li><li>Xin, Y., 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=BPS:+a+database+of+RNA+base-pair+structures.">BPS: a database of RNA base-pair structures.</a> Nucleic Acids Res. 37, D83-D88 (2009).</li><li>Zheng, G., Colasanti, A. V., 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=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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H., Petkeviciute, D., Zakrzewska, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+analysis+of+nucleic+acids+revisited:+Curves+.">Conformational analysis of nucleic acids revisited: Curves+.</a> Nucleic Acids Res. 37, 5917-5929 (2009).</li><li>Franklin, R. E., Gosling, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+configuration+in+sodium+thymonucleate.">Molecular configuration in sodium thymonucleate.</a> Nature. 171, 740-741 (1953).</li><li>Watson, J. D., Crick, F. H. 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R., Schneider, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Nucleic+Acid+Database:+a+comprehensive+relational+database+of+three-dimensional+structures+of+nucleic+acids.">The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids.</a> Biophys. J. 63, 751-759 (1992).</li><li>Stella, S., Cascio, D., Johnson, R. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+shape+of+the+DNA+minor+groove+directs+binding+by+the+DNA-bending+protein+Fis.">The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.</a> Genes Dev. 24, 814-826 (2010).</li><li>Swigon, D., Coleman, B. D., 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=Modeling+the+Lac+repressor-operator+assembly:+the+influence+of+DNA+looping+on+Lac+repressor+conformation.">Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.</a> Proc. Natl. Acad. Sci. U.S.A. 103, 9879-9884 (2006).</li><li>Czapla, L., Swigon, D., 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=Effects+of+the+nucleoid+protein+HU+on+the+structure,+flexibility,+and+ring-closure+properties+of+DNA+deduced+from+Monte-Carlo+simulations.">Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations.</a> J. Mol. Biol. 382, 353-370 (2008).</li><li>Czapla, L., Peters, J. P., Rueter, E. M., Olson, W. K., Maher, L. 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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ARTS+web+server+for+aligning+RNA+tertiary+structures.">The ARTS web server for aligning RNA tertiary structures.</a> Nucleic Acids Res. 34, 412-415 (2006).</li><li>Dixit, S. B., Beveridge, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+bioinformatics+of+DNA:+a+web-based+tool+for+the+analysis+of+molecular+dynamics+results+and+structure+prediction.">Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction.</a> Bioinformatics. 22, 1007-1009 (2006).</li><li>de Vries, S. J., van Dijk, M., Bonvin, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HADDOCK+web+server+for+data-driven+biomolecular+docking.">The HADDOCK web server for data-driven biomolecular docking.</a> Nat. Protoc. 5, 883-897 (2010).</li><li>Capriotti, E., Marti-Renom, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SARA:+a+server+for+function+annotation+of+RNA+structures.">SARA: a server for function annotation of RNA structures.</a> Nucleic Acids Res. 37, 260-265 (2009).</li><li>van Dijk, M., Bonvin, A. 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在这篇文章中提出的协议集，只触及3DNA程序套件的能力。的工具，可以适用核糖核酸结构识别非经典的碱基对，以确定的二级结构的上下文中，会发生这样的配对，量化螺旋片段的空间配置，测量沿链主链的碱基重叠，等等。 rebuild命令允许用户构建简单和翔实的基地和基地对像中的插图所示， 图1块表示。建设工具还包括在一个给定的结构化模板功能，以“线”不同的序列，产生无...

了解三维结构的DNA，RNA和蛋白，药物和其他配体的配合物，用于解密其不同的生物功能是至关重要的，允许设计合理的治疗学。这种结构的探索需要三个单独的，但密切相关的部分组成：分析（提取型态的形状和相互作用），建模（评估能量和分子动力学），和可视化。结构分析和模型建设基本上同一枚硬币的两面，他们两个补充和可视化。 3DNA一套计算机程序，是一个日益流行的结构与功能的生物信息学工具包，分析，构建和可视化三维核酸结构。早期出版物概述软件1，提供的食谱执行所选任务2的功能，介绍了基于Web的界面软件的流行特点，结构特点数据库收集使用 3DNA 4，5和示出的软件的实用程序在分析中的DNA和RNA结构6，7。 本文目的是把的3DNA软件套件实验室科学家和其他人的利益和/或需要调查的DNA和RNA的空间组织与国家的最先进的计算工具。这里提出的协议包括一步一步的说明（一）下载并安装一个Mac OS X系统上的软件，（II-III）DNA碱基对组成的步骤，水平结构分析和修改（ IV-V），以分析和相关的DNA结构调整套，及（vi）与用户友好的w3DNA Web界面蛋白质修饰过的DNA链构建模型。软件具有分析能力，解决个别结构，利用X射线晶体学方法以及大型利用核磁共振（NMR）方法测定结构或计算机仿真技术所产生的合奏。 这里的结构检查包括（i）的高分辨率晶体结构的DNA势必到HBB蛋白从伯氏疏螺旋体 （蜱传播的细菌，导致莱姆病在人类9，10），（二）两个大组顺序相关的DNA分子与分子模拟11 - 4500快照d的（GGCAAAATTTTGCC）的，2和d（CCGTTTTAAAACGG）2在100皮秒为单位收集，在计算过程中，及（iii）O3 DNA操作员基于NMR的结构的一个小的合奏绑定的头饰在大肠杆菌 lac阻遏蛋白12。下面的说明包括有关如何访问这些结构，以及如何使用3DNA（此文件的一个副本被发现相关文件的原子坐标信息3DNA在<a href="http://forum.x3dna.org/jove" target="_blank">http://forum.x3dna.org/jove</a>论坛）审查和修改这些结构。

analyzing and building nucleic acid structures with 3dna

追梦的软件包是一个流行和通用的生物信息学工具与功能分析，构建，可视化三维核酸结构。本文提出了详细的协议的一个子集3DNA提供新的和流行的特点，适用于个别结构和相关结构的合奏。协议1列出下载并安装该软件所需要的指令的集合。其次，协议2，通过分析的核酸结构，包括碱基对的分配和确定刚体参数描述结构，协议3，由一个原子的重建的说明模型的结构从它的刚体参数。追梦，版本2.1，最新版本的结构歌舞团的分析和操作的新功能，如核磁共振（NMR）测量和分子动力学（MD推导出）模拟，这些功能在协议中的4和5。除了 ​​追梦的独立软件包，w3DNA位于<a href="http://w3dna.rutgers.edu" target="_blank">http://w3dna.rutgers.edu</a> ， web服务器，提供了一个友好的用户界面功能的软件选择。协议6演示了一个新的功能的网站建设模型长的DNA结合蛋白的分子修饰在用户指定的位置。

常规使用的的3DNA软件工具来分析核酸结构。例如，碱基对的身份和特征在双螺旋片段的碱基的DNA和RNA结构的安排刚体参数自动计算，为每一个新的条目存储在核酸数据库22，世界范围内的存储库核酸的结构信息。刚体参数确定协议2的值轻易表露在三维结构的扭曲，如极端的DNA大沟，大正滚动角（64.95°，60.93°）弯曲成两个网站，发现在AT·AT与伯氏疏螺旋体 HBB蛋白8（ ?...

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

追梦的软件包是一个流行和通用的生物信息学工具与功能分析，构建，可视化三维核酸结构。本文提出了详细的协议的一个子集3DNA提供新的和流行的特点，适用于个别结构和相关结构的合奏。

核酸结构分析及建设3DNA

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Differential Imaging of Biological Structures with Doubly-resonant Coherent Anti-stokes Raman Scattering (CARS)

Differential Imaging of Biological Structures with Doubly-resonant Coherent Anti-stokes Raman Scattering CARS

差分成像生物结构与双共振相干反斯托克斯拉曼散射（CARS）

Coherent Raman imaging techniques have seen a dramatic increase in activity over the past decade due to their promise to enable label-free optical imaging ...

Electricity-Free, Sequential Nucleic Acid and Protein Isolation

免电力，顺序的核酸和蛋白质的分离

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern ...

Simultaneous Multicolor Imaging of Biological Structures with Fluorescence Photoactivation Localization Microscopy

Localization-based super resolution microscopy can be applied to obtain a spatial map (image) of the distribution of individual fluorescently labeled ...

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

核酸，蛋白质与甲基转移和辅酶类似物序列特异性标签

S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific ...

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

数字核酸定量实验分析的简单堆积读数

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are ...

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

高效的核酸提取和16S rRNA基因序列的细菌群落特征

There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing ...

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

激光捕获微分块RNA-测序空间和时间组织特异性基因表达分析

The development of a complex multicellular organism is governed by distinct cell types that have different transcriptional profiles. To identify ...