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

Vi er taknemmelige for Jiří Sponsor til deling koordinaterne af DNA dobbelt helix genereret i molekylære simuleringer. Vi anerkender også Nada Spackova om bistand til at downloade disse strukturer. Til støtte for dette arbejde gennem USPHS forskningsbevillinger GM34809 og GM096889 er taknemmeligt anerkendt.

1.. Installation af softwarepakke <ol><li> Tilslut til 3DNA hjemmeside på <a href="http://x3dna.org" target="_blank">http://x3dna.org</a> og klik på linket til 3DNA Forum. Inden forummet vælge &#39;register&#39; linket og følg anvisningerne for at oprette en ny konto. </li><li> Følgende anvisninger detalje installation af softwaren på en OS X-baseret Macintosh-computer med et default &#39;bash&#39; shell. Proceduren for Linux eller Windows (Cygwin, MinGW / MSYS) systemer med almindeligt anvendte skaller (herunde...

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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. 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Det sæt af protokoller, der præsenteres i denne artikel kun berøre mulighederne i 3DNA suite af programmer. Værktøjerne kan anvendes til RNA strukturer at identificere ikke-kanoniske basepar, at bestemme de sekundære strukturelle sammenhænge, ​​hvor en sådan parring forekommer, at kvantificere den rumlige disponering af spiralformede fragmenter, at måle overlapningen af ​​baser langs kæden rygrad, osv. Ombygningen kommandoen tillader brugeren at konstruere enkle og informative blok repræsentationer af...

Forståelse af de tre-dimensionelle strukturer af DNA, RNA og deres komplekser med proteiner, narkotika og andre ligander, er afgørende for at decifrere deres forskellige biologiske funktioner, og som giver mulighed rationelt design af lægemidler. Udforskning af sådanne strukturer indebærer tre separate, men nært beslægtede komponenter: analyse (for at udvinde mønstre i figurer og interaktioner), modellering (at vurdere energetik og molekylær dynamik), og visualisering. Strukturel analyse og model bygning er grundlæggende to sider af samme mønt, og visualisering supplerer dem begge. Den 3DNA suite af edb-programmer er en stadig mere populær strukturel bioinformatik værktøjskasse med kapaciteter til at analysere, konstruere, og visualisere tredimensionelle nukleinsyrestrukturer. Tidligere publikationer skitseret mulighederne i softwaren 1, forudsat opskrifter til at udføre udvalgte opgaver 2, indførte den web-baserede brugerfladetil populære funktioner i softwaren 3, indsamlet præsenteret databaser af strukturelle træk ved hjælp 3DNA 4, 5 og illustreret nytten af softwaren i analysen af både DNA og RNA-strukturer 6, 7. Målet med denne artikel er at bringe 3DNA software kit til at laboranter og andre med interesser og / eller behov for at undersøge DNA og RNA rumlig organisation med state-of-the-art beregningsværktøjer. De protokoller, der præsenteres her, inkluderer trin-for-trin instruktioner (i) at downloade og installere softwaren på en Mac OS X-system, (ii-iii) at analysere og ændre DNA strukturer på niveau med de indgående basepar trin, ( iv-v) at analysere og tilpasse sæt af relaterede DNA strukturer, og (vi) at konstruere modeller for protein-dekoreret DNA kæder med den brugervenlige w3DNA web interface. Den software har evnen til at analysere de enkelte strukturer løses ved hjælp røntgenkrystallografiske metoder samt storensembler af konstruktioner bestemt med kernemagnetisk resonans (NMR) metoder eller genereret af computer-simulering teknikker. Strukturerne undersøgte her omfatter (i) høj opløsning krystalstruktur af DNA bundet til Hbb protein fra Borrelia burgdorferi 8 (tick-bårne bakterie, der forårsager Lyme sygdom hos mennesker 9, 10), (ii) to store sæt sekventielt relaterede DNA-molekyler fremstillet med molekylære simuleringer 11 - 4.500 snapshots af d (GGCAAAATTTTGCC) 2 og d (CCGTTTTAAAACGG) 2 opsamlet i 100 psec intervaller for beregningerne, og (iii) en lille ensemble af NMR-baserede strukturer O3 DNA operatør bundet til headpieces af Escherichia coli Lac repressorproteinet 12. Instruktionerne nedenfor indeholde oplysninger om, hvordan du får adgang til filer af atomkoordinater forbundet med hver af disse strukturer samt hvordan man bruger 3DNA (en kopi af denne fil er fundetpå 3DNA forum på <a href="http://forum.x3dna.org/jove" target="_blank">http://forum.x3dna.org/jove</a> ) at undersøge og ændre disse strukturer.

analyzing and building nucleic acid structures with 3dna

Den 3DNA softwarepakke er en alsidig og populær bioinformatik værktøj med kapaciteter til at analysere, konstruere og visualisere tredimensionale nukleinsyrestrukturer. Denne artikel præsenterer detaljerede protokoller for en delmængde af nye og populære funktioner i 3DNA, der gælder for både individuelle strukturer og ensembler af relaterede strukturer. Protokol 1 viser det sæt af instruktioner, der er nødvendige for at downloade og installere softwaren. Dette følges, i protokol 2, til analyse af en nukleinsyre struktur, herunder tildeling af basepar og bestemmelse af stive-krop parametre, der beskriver strukturen, og i protokol 3, med en beskrivelse af genopbygningen af ​​en atomar model af en struktur fra dens stive kropsparametre. Den seneste version af 3DNA, version 2.1, har nye funktioner til analyse og manipulation af ensembler af strukturer, såsom dem udledes kernemagnetisk resonans (NMR) målinger og molekylær dynamik (MD) Simuleringer, disse funktioner er præsenteret i protokol 4 og 5. Ud over den 3DNA stand-alone-software pakken, w3DNA webserveren, placeret på <a href="http://w3dna.rutgers.edu" target="_blank">http://w3dna.rutgers.edu</a> tilvejebringer en brugervenlig grænseflade til udvalgte funktioner i softwaren. Protokol 6 viser en roman træk ved webstedet for at bygge modeller af lange DNA-molekyler dekoreret med bundne proteiner bruger-angivne steder.

De 3DNA softwareværktøjer anvendes rutinemæssigt til at analysere nukleinsyrestrukturer. For eksempel er identitet basepar og den stive-krop parametre, der kendetegner arrangementer af baser i dobbelt heliske fragmenter af DNA og RNA-strukturer automatisk beregnes og gemmes for hver ny post i Nucleic Acid Database 22, en verdensomspændende samling af nukleinsyre strukturel information. Værdierne af rigid body parametre bestemmes med protokol 2 let afsløre forvridninger i tredimensionel struktur, såsom ...

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

Den 3DNA softwarepakke er en alsidig og populær bioinformatik værktøj med kapaciteter til at analysere, konstruere og visualisere tredimensionale nukleinsyrestrukturer. Denne artikel præsenterer detaljerede protokoller for en delmængde af nye og populære funktioner i 3DNA, der gælder for både individuelle strukturer og ensembler af relaterede strukturer.

Analysere og Building nukleinsyrestrukturer med 3DNA

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

Sekvens-specifik mærkning af nukleinsyrer og proteiner med methyltransferaser og cofaktor Analoger

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

Enkel Bulk Udlæsning af digitale Nucleic Acid Kvantificering Analyser

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

Effektiv Nucleic Acid Udvinding og 16S rRNA Gene sekventering for bakteriel Community karakterisering

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