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1yfv

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(New page: 200px<br /><applet load="1yfv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yfv" /> '''STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3...)
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[[Image:1yfv.gif|left|200px]]<br /><applet load="1yfv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yfv" />
 
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'''STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE'''<br />
 
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==Overview==
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==STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE==
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The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif, in the secondary structures of biological RNAs. The three-dimensional, structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy, minimization with NMR-derived restraints for 78 interproton distances (per, strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26, dihedral angles (per strand). The G x A mismatch structures are similar to, those observed in a DNA duplex [Li, Y., Zon, G., &amp; Wilson, W. D. (1991), Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., &amp; Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine, 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G, 2-amino and A 6-amino protons are within hydrogen-bonding distance of a, phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and, G-G stacking is observed between the G x A mismatches. This contrasts with, the poor stacking observed between the G x A mismatches and closing G x C, base pairs. The stems are basically A-form with all bases in the anti, conformation and all nonterminal sugars in the C3'-endo conformation. The, structure rationalizes previous thermodynamic, circular dichroism, and, imino proton NMR results and suggests tandem G x A mismatches in RNA may, provide a contact site for tertiary interactions.
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<StructureSection load='1yfv' size='340' side='right'caption='[[1yfv]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yfv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFV 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=1yfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfv OCA], [https://pdbe.org/1yfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfv RCSB], [https://www.ebi.ac.uk/pdbsum/1yfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfv ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., &amp; Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., &amp; Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions.
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==About this Structure==
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Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics.,SantaLucia J Jr, Turner DH Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:8251479<ref>PMID:8251479</ref>
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1YFV is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YFV OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics., SantaLucia J Jr, Turner DH, Biochemistry. 1993 Nov 30;32(47):12612-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8251479 8251479]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1yfv" style="background-color:#fffaf0;"></div>
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[[Category: Junior, J.Santalucia.]]
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== References ==
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[[Category: Turner, D.H.]]
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<references/>
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[[Category: 2-d nmr]]
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__TOC__
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[[Category: anti-parallel rna duplex]]
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</StructureSection>
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[[Category: g:a mismatch]]
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[[Category: Large Structures]]
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[[Category: ribonucleic acid]]
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[[Category: Synthetic construct]]
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[[Category: Santalucia Junior J]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:04:50 2007''
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[[Category: Turner DH]]

Current revision

STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE

PDB ID 1yfv

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