1db6

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[[Image:1db6.gif|left|200px]]
[[Image:1db6.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1db6 |SIZE=350|CAPTION= <scene name='initialview01'>1db6</scene>
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The line below this paragraph, containing "STRUCTURE_1db6", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1db6| PDB=1db6 | SCENE= }}
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|RELATEDENTRY=[[2arg|2ARG]], [[1old|1OLD]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1db6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1db6 OCA], [http://www.ebi.ac.uk/pdbsum/1db6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1db6 RCSB]</span>
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}}
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'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''
'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''
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==About this Structure==
==About this Structure==
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1DB6 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DB6 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DB6 OCA].
==Reference==
==Reference==
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]
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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[[Category: Protein complex]]
 
[[Category: Frankel, A D.]]
[[Category: Frankel, A D.]]
[[Category: Harada, K.]]
[[Category: Harada, K.]]
[[Category: Robertson, S A.]]
[[Category: Robertson, S A.]]
[[Category: Wemmer, D E.]]
[[Category: Wemmer, D E.]]
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[[Category: aptamer]]
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[[Category: Aptamer]]
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[[Category: argininamide]]
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[[Category: Argininamide]]
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[[Category: arginine]]
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[[Category: Arginine]]
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[[Category: hairpin]]
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[[Category: Hairpin]]
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[[Category: nmr]]
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[[Category: Nmr]]
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[[Category: selex]]
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[[Category: Selex]]
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[[Category: single-strand]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:38:09 2008''
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Revision as of 10:39, 2 May 2008

Image:1db6.gif

Template:STRUCTURE 1db6

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


Overview

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.

About this Structure

Full crystallographic information is available from OCA.

Reference

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 Page seeded by OCA on Fri May 2 13:39:08 2008

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