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| | ==The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs== | | ==The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs== |
| - | <StructureSection load='2o83' size='340' side='right'caption='[[2o83]], [[NMR_Ensembles_of_Models | 18 NMR models]]' scene=''> | + | <StructureSection load='2o83' size='340' side='right'caption='[[2o83]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2o83]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O83 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2O83 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2o83]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O83 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IC:ISOCYTIDINE-5-MONOPHOSPHATE'>IC</scene>, <scene name='pdbligand=IG:ISOGUANOSINE-5-MONOPHOSPHATE'>IG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2o81|2o81]]</td></tr> | + | <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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2o83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o83 OCA], [http://pdbe.org/2o83 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2o83 RCSB], [http://www.ebi.ac.uk/pdbsum/2o83 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2o83 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2o83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o83 OCA], [https://pdbe.org/2o83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o83 RCSB], [https://www.ebi.ac.uk/pdbsum/2o83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o83 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kennedy, S D]] | + | [[Category: Kennedy SD]] |
| - | [[Category: Turner, D H]] | + | [[Category: Turner DH]] |
| - | [[Category: Imino ga pair]]
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| - | [[Category: Isocytidine]]
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| - | [[Category: Isoguanosine]]
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| - | [[Category: Rna]]
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| - | [[Category: Secondary structure prediction]]
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| - | [[Category: Thermodynamic]]
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| Structural highlights
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chen G, Kierzek R, Yildirim I, Krugh TR, Turner DH, Kennedy SD. 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. J Phys Chem B. 2007 Jun 21;111(24):6718-27. Epub 2007 Apr 6. PMID:17411085 doi:10.1021/jp068732m
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