2o4y

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[[Image:2o4y.png|left|200px]]
 
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{{STRUCTURE_2o4y| PDB=2o4y | SCENE= }}
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==Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide==
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<StructureSection load='2o4y' size='340' side='right'caption='[[2o4y]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2o4y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O4Y FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCX:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-NITRO-1H-INDOLE-3-CARBOXAMIDE'>NCX</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2o4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o4y OCA], [https://pdbe.org/2o4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o4y RCSB], [https://www.ebi.ac.uk/pdbsum/2o4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o4y ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Universal bases hybridize with all other natural DNA or RNA bases, and have applications in PCR and sequencing. We have analysed by nuclear magnetic resonance spectroscopy the structure and dynamics of three DNA oligonucleotides containing the universal base analogues 5-nitroindole and 5-nitroindole-3-carboxamide. In all systems studied, both the 5-nitroindole nucleotide and the opposing nucleotide adopt a standard anti conformation and are fully stacked within the DNA duplex. The 5-nitroindole bases do not base pair with the nucleotide opposite them, but intercalate between this base and an adjacent Watson-Crick pair. In spite of their smooth accommodation within the DNA double-helix, the 5-nitroindole-containing duplexes exist as a dynamic mixture of two different stacking configurations exchanging fast on the chemical shift timescale. These configurations depend on the relative intercalating positions of the universal base and the opposing base, and their exchange implies nucleotide opening motions on the millisecond time range. The structure of these nitroindole-containing duplexes explains the mechanism by which these artificial moieties behave as universal bases.
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===Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide===
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Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide.,Gallego J, Loakes D Nucleic Acids Res. 2007;35(9):2904-12. Epub 2007 Apr 16. PMID:17438041<ref>PMID:17438041</ref>
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{{ABSTRACT_PUBMED_17438041}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 2o4y" style="background-color:#fffaf0;"></div>
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[[2o4y]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O4Y OCA].
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== References ==
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<references/>
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==Reference==
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__TOC__
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<ref group="xtra">PMID:017438041</ref><references group="xtra"/>
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</StructureSection>
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[[Category: Gallego, J.]]
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[[Category: Large Structures]]
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[[Category: Loakes, D.]]
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[[Category: Synthetic construct]]
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[[Category: Dna]]
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[[Category: Gallego J]]
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[[Category: Dna universal base nitroindole intercalation dynamic]]
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[[Category: Loakes D]]

Current revision

Solution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide

PDB ID 2o4y

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