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| ==RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG== | | ==RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG== |
| <StructureSection load='6n8f' size='340' side='right'caption='[[6n8f]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | | <StructureSection load='6n8f' size='340' side='right'caption='[[6n8f]]' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[6n8f]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N8F FirstGlance]. <br> | | <table><tr><td colspan='2'>[[6n8f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N8F FirstGlance]. <br> |
| </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=6n8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8f OCA], [http://pdbe.org/6n8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n8f RCSB], [http://www.ebi.ac.uk/pdbsum/6n8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8f ProSAT]</span></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'>[https://proteopedia.org/fgij/fg.htm?mol=6n8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n8f OCA], [https://pdbe.org/6n8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n8f RCSB], [https://www.ebi.ac.uk/pdbsum/6n8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n8f ProSAT]</span></td></tr> |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| RNA thermodynamics play an important role in determining the two- and three-dimensional structures of RNA. Internal loops of the sequence 5'-GMNU/3'-UNMG are relatively unstable thermodynamically. Here, five duplexes with GU-flanked 2 x 2 nucleotide internal loops were structurally investigated to reveal determinants of their instability. The following internal loops were investigated: 5'-GCAU/3'-UACG, 5'-UUCG/3'-GCUU, 5'-GCUU/3'-UUCG, 5'-GUCU/3'-UCUG, and 5'-GCCU/3'-UCCG. Two-dimensional nuclear magnetic resonance spectra indicate the absence of GU wobble base pairing in 5'-GCUU/3'-UUCG, 5'-GUCU/3'-UCUG, and 5'-GCCU/3'-UCCG. The 5'-GCUU/3'-UUCG loop has an unusual conformation of the GU base pairs, in which U's O2 carbonyl forms a bifurcated hydrogen bond with G's amino and imino protons. The internal loop of 5'-GUCU/3'-UCUG displays a shifted configuration in which GC pairs flank a U-U pair and several U's are in fast exchange between positions inside and outside the helix. In contrast, 5'-GCAU/3'-UACG and 5'-UUCG/3'-GCUU both have the expected GU wobble base pairs flanking the internal loop. Evidently, GU base pairs flanking internal loops are more likely to display atypical structures relative to Watson-Crick base pairs flanking internal loops. This appears to be more likely when the G of the GU pair is 5' to the loop. Such unusual structures could serve as recognition elements for biological function and as benchmarks for structure prediction methods.
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| Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.,Berger KD, Kennedy SD, Turner DH Biochemistry. 2019 Jan 31. doi: 10.1021/acs.biochem.8b01027. PMID:30702283<ref>PMID:30702283</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 6n8f" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Berger, K D]] | | [[Category: Unidentified]] |
| [[Category: Kennedy, S D]] | | [[Category: Berger KD]] |
| [[Category: Turner, D H]] | | [[Category: Kennedy SD]] |
| [[Category: Bifurcated gu]] | | [[Category: Turner DH]] |
| [[Category: Duplex]]
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| [[Category: Internal loop]]
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| [[Category: Rna]]
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| [[Category: Uc pair]]
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