2ky2: Difference between revisions

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[[Image:2ky2.png|left|200px]]


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==The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU==
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<StructureSection load='2ky2' size='340' side='right'caption='[[2ky2]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ky2]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KY2 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ky2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ky2 OCA], [https://pdbe.org/2ky2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ky2 RCSB], [https://www.ebi.ac.uk/pdbsum/2ky2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ky2 ProSAT]</span></td></tr>
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== Publication Abstract from PubMed ==
ABSTRACT: Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)2, (rGACUAGAGUCA)2, (rGACAAGUGUCA)2, (rGGUAGGCCA)2 and (rGACGAGUGUCA)2. The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC)2 (Wu, M., SantaLucia, Jr., J. and Turner, D. H. (1997) Biochemistry 36: 4449-4460). For loops bounded by Watson-Crick pairs, the AG and Watson-Crick pairs are all head-to-head imino-paired (cis Watson-Crick/Watson-Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen bonding interactions. Of the two loops bounded by G-U pairs, only the 5 UAGG/3 GGAU loop adopts canonical UG wobble pairing (cis Watson-Crick/Watson-Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5 GAGU/3 UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA)2) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson-Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in an undetermined conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.


===The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU===
RNA Internal Loops with Tandem AG Pairs: The Structure of the 5 GAGU/3 UGAG Loop can be Dramatically Different from Others, Including 5 AAGU/3 UGAA.,Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD Biochemistry. 2010 May 20. PMID:20481618<ref>PMID:20481618</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
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<references/>
{{ABSTRACT_PUBMED_20481618}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2KY2 is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KY2 OCA].
[[Category: Hammond NB]]
 
[[Category: Kennedy SD]]
==Reference==
[[Category: Turner DH]]
<ref group="xtra">PMID:20481618</ref><references group="xtra"/>
[[Category: Hammond, N B.]]
[[Category: Kennedy, S D.]]
[[Category: Turner, D H.]]
[[Category: Dual syn gg pair]]
[[Category: Extrahelical u]]
[[Category: Imino ag pair]]
[[Category: Rna]]
[[Category: Tandem ag pair]]
[[Category: Thermodynamic]]
 
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