1db6

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(New page: 200px<br /><applet load="1db6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1db6" /> '''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGA...)
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'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''<br />
'''SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE'''<br />
==Overview==
==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.
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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.
==About this Structure==
==About this Structure==
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1DB6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with AAR as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DB6 OCA].
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1DB6 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=AAR:'>AAR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10653638 10653638]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: Frankel, A.D.]]
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[[Category: Frankel, A D.]]
[[Category: Harada, K.]]
[[Category: Harada, K.]]
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[[Category: Robertson, S.A.]]
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[[Category: Robertson, S A.]]
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[[Category: Wemmer, D.E.]]
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[[Category: Wemmer, D E.]]
[[Category: AAR]]
[[Category: AAR]]
[[Category: aptamer]]
[[Category: aptamer]]
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[[Category: single-strand]]
[[Category: single-strand]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:54:53 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:14:49 2008''

Revision as of 10:14, 21 February 2008

Image:1db6.gif

1db6

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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

1DB6 is a Protein complex structure of sequences from [1] with as ligand. 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 Thu Feb 21 12:14:49 2008

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