View source for 1xv0


==Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG==
<StructureSection load='1xv0' size='340' side='right'caption='[[1xv0]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1xv0]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XV0 FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></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=1xv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv0 OCA], [https://pdbe.org/1xv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xv0 RCSB], [https://www.ebi.ac.uk/pdbsum/1xv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv0 ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Internal loops in RNA are important for folding and function. Many folding motifs are internal loops containing GA base pairs, which are usually thermodynamically stabilizing, i.e., contribute favorable free energy to folding. Understanding the sequence dependence of folding stability and structure in terms of molecular interactions, such as hydrogen bonding and base stacking, will provide a foundation for predicting stability and structure. Here, we report the NMR structure of the oligonucleotide duplex, 5'GGUGGAGGCU3'/3'PCCGAAGCCG5' (P = purine), containing an unusually stable and relatively abundant internal loop, 5'GGA3'/3'AAG5'. This loop contains three consecutive sheared GA pairs (trans Hoogsteen/Sugar edge AG) with separate stacks of three G's and three A's in a row. The thermodynamic consequences of various nucleotide substitutions are also reported. Significant destabilization of approximately 2 kcal/mol at 37 degrees C is found for substitution of the middle GA with AA to form 5'GAA3'/3'AAG5'. This destabilization correlates with a unique base stacking and hydrogen-bonding network within the 5'GGA3'/3'AAG5' loop. Interestingly, the motifs, 5'UG3'/3'GA5' and 5'UG3'/3'AA5', have stability similar to 5'CG3'/3'GA5' even though UG and UA pairs are usually less stable than CG pairs. Consecutive sheared GA pairs in the 5'GGA3'/3'AAG5' loop are preorganized for potential tertiary interactions and ligand binding.

Solution structure of an RNA internal loop with three consecutive sheared GA pairs.,Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH Biochemistry. 2005 Mar 1;44(8):2845-56. PMID:15723528<ref>PMID:15723528</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1xv0" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Chen G]]
[[Category: Kennedy SD]]
[[Category: Krugh TR]]
[[Category: Turner DH]]
[[Category: Znosko BM]]