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| | ==Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2== | | ==Sheared A(anti)-A(anti) Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2== |
| - | <StructureSection load='1muv' size='340' side='right' caption='[[1muv]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1muv' size='340' side='right'caption='[[1muv]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1muv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MUV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1muv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MUV FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yfv|1yfv]], [[1gid|1gid]], [[1mv1|1mv1]], [[1mv2|1mv2]], [[1mv6|1mv6]]</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1muv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1muv OCA], [http://pdbe.org/1muv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1muv RCSB], [http://www.ebi.ac.uk/pdbsum/1muv PDBsum]</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=1muv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1muv OCA], [https://pdbe.org/1muv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1muv RCSB], [https://www.ebi.ac.uk/pdbsum/1muv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1muv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Burkard, M E]] | + | [[Category: Large Structures]] |
| - | [[Category: Krugh, T R]] | + | [[Category: Burkard ME]] |
| - | [[Category: Schroeder, S J]] | + | [[Category: Krugh TR]] |
| - | [[Category: Turner, D H]] | + | [[Category: Schroeder SJ]] |
| - | [[Category: Znosko, B M]] | + | [[Category: Turner DH]] |
| - | [[Category: Aa mismatch]] | + | [[Category: Znosko BM]] |
| - | [[Category: Duplex]]
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| - | [[Category: Ribonucleic acid]]
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| - | [[Category: Rna]]
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| - | [[Category: Tandem mismatch]]
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| Structural highlights
Publication Abstract from PubMed
The 5'(rGGCAAGCCU)(2) duplex contains tandem A.A pairs. The three-dimensional structure of the 5'(rGGCAAGCCU)(2) duplex was modeled by molecular dynamics and energy minimization with NMR-derived distance and dihedral angle restraints. Although the 5'(rCAAG)(2) loop is thermodynamically destabilizing by 1.1 kcal/mol, the tandem A.A pairs adopt a predominant conformation: a sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment similar to that observed in the crystal structure of the P4-P6 domain of the Tetrahymena thermophila intron [Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Science 273, 1678-1685]. The NMR-derived structure of the 5'(rGGCAAGCCU)(2) duplex exhibits cross-strand hydrogen bonds from N3 of A4 to an amino hydrogen of A5 and from the 2' oxygen of the A4 sugar to the other amino hydrogen of A5. An intrastrand hydrogen bond is formed from the 2' OH hydrogen of A4 to O5' of A5. The cross-strand A5 bases are stacked. The Watson-Crick G-C regions are essentially A-form. The sheared anti-anti (A.A trans Hoogsteen/Sugar-edge) alignment provides potential contact sites for tertiary interactions and, therefore, is a possible target site for therapeutics. Thus, thermodynamically destabilizing internal loops can be preorganized for tertiary interactions or ligand binding.
Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2.,Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:12475246[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Znosko BM, Burkard ME, Schroeder SJ, Krugh TR, Turner DH. Sheared Aanti.Aanti base pairs in a destabilizing 2 x 2 internal loop: the NMR structure of 5'(rGGCAAGCCU)2. Biochemistry. 2002 Dec 17;41(50):14969-77. PMID:12475246
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