1db6

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[[Image:1db6.gif|left|200px]]
 
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==SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE==
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The line below this paragraph, containing "STRUCTURE_1db6", creates the "Structure Box" on the page.
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<StructureSection load='1db6' size='340' side='right'caption='[[1db6]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1db6]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DB6 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene></td></tr>
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{{STRUCTURE_1db6| PDB=1db6 | SCENE= }}
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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=1db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1db6 OCA], [https://pdbe.org/1db6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1db6 RCSB], [https://www.ebi.ac.uk/pdbsum/1db6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1db6 ProSAT]</span></td></tr>
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</table>
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'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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The structure of a DNA aptamer, which was selected for specific binding to arginine, was determined using NMR spectroscopy. The sequence forms a hairpin loop, with residues important for binding occurring in the loop region. Binding of argininamide induces formation of one Watson-Crick and two non-Watson-Crick base pairs, which facilitate generation of a binding pocket. The specificity for arginine seems to arise from contacts between the guanidino end of the arginine and phosphates, with atoms positioned by the shape of the pocket. Complex binding kinetics are observed suggesting that there is a slow interconversion of two forms of the DNA, which have different binding affinities. These data provide information on the process of adaptive recognition of a ligand by an aptamer.
The structure of a DNA aptamer, which was selected for specific binding to arginine, was determined using NMR spectroscopy. The sequence forms a hairpin loop, with residues important for binding occurring in the loop region. Binding of argininamide induces formation of one Watson-Crick and two non-Watson-Crick base pairs, which facilitate generation of a binding pocket. The specificity for arginine seems to arise from contacts between the guanidino end of the arginine and phosphates, with atoms positioned by the shape of the pocket. Complex binding kinetics are observed suggesting that there is a slow interconversion of two forms of the DNA, which have different binding affinities. These data provide information on the process of adaptive recognition of a ligand by an aptamer.
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==About this Structure==
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Structure determination and binding kinetics of a DNA aptamer-argininamide complex.,Robertson SA, Harada K, Frankel AD, Wemmer DE Biochemistry. 2000 Feb 8;39(5):946-54. PMID:10653638<ref>PMID:10653638</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DB6 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 determination and binding kinetics of a DNA aptamer-argininamide complex., Robertson SA, Harada K, Frankel AD, Wemmer DE, Biochemistry. 2000 Feb 8;39(5):946-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10653638 10653638]
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</div>
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[[Category: Frankel, A D.]]
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<div class="pdbe-citations 1db6" style="background-color:#fffaf0;"></div>
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[[Category: Harada, K.]]
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== References ==
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[[Category: Robertson, S A.]]
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<references/>
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[[Category: Wemmer, D E.]]
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__TOC__
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[[Category: Aptamer]]
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</StructureSection>
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[[Category: Argininamide]]
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[[Category: Large Structures]]
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[[Category: Arginine]]
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[[Category: Frankel AD]]
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[[Category: Hairpin]]
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[[Category: Harada K]]
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[[Category: Nmr]]
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[[Category: Robertson SA]]
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[[Category: Selex]]
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[[Category: Wemmer DE]]
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[[Category: Single-strand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:39:08 2008''
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Current revision

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

PDB ID 1db6

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