2o81

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(New page: 200px<br /><applet load="2o81" size="350" color="white" frame="true" align="right" spinBox="true" caption="2o81" /> '''The Structure of Tandem GA RNA Pairs When Fl...)
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[[Image:2o81.gif|left|200px]]<br /><applet load="2o81" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2o81" />
 
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'''The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs'''<br />
 
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==Overview==
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==The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs==
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The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl, groups transposed relative to the Watson-Crick GC pair, provides an, expanded alphabet for understanding interactions that shape nucleic acid, structure. Here, thermodynamic stabilities of tandem GA pairs flanked by, iGiC pairs are reported along with the NMR structures of the RNA, self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared, GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in, (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino, and sheared GA pairs flanked by GC pairs in the RNA self-complementary, duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC, substitutions result in less favorable loop stability. The results provide, benchmarks for testing computations of molecular interactions that shape, RNA three-dimensional structure.
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<StructureSection load='2o81' size='340' side='right'caption='[[2o81]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2o81]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O81 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=IC:ISOCYTIDINE-5-MONOPHOSPHATE'>IC</scene>, <scene name='pdbligand=IG:ISOGUANOSINE-5-MONOPHOSPHATE'>IG</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=2o81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o81 OCA], [https://pdbe.org/2o81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o81 RCSB], [https://www.ebi.ac.uk/pdbsum/2o81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o81 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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The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure.
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==About this Structure==
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Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.,Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD J Phys Chem B. 2007 Jun 21;111(24):6718-27. Epub 2007 Apr 6. PMID:17411085<ref>PMID:17411085</ref>
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2O81 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O81 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs., Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD, J Phys Chem B. 2007 Jun 21;111(24):6718-27. Epub 2007 Apr 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17411085 17411085]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2o81" style="background-color:#fffaf0;"></div>
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[[Category: Chen, G.]]
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== References ==
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[[Category: Turner, D.H.]]
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<references/>
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[[Category: isocytidine]]
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__TOC__
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[[Category: isoguanosine]]
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</StructureSection>
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[[Category: rna]]
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[[Category: Large Structures]]
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[[Category: secondary structure prediction]]
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[[Category: Chen G]]
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[[Category: sheared ga pair]]
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[[Category: Turner DH]]
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[[Category: thermodynamics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:35:35 2008''
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The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs

PDB ID 2o81

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