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| - | [[Image:2au4.gif|left|200px]] | + | {{Seed}} |
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| | {{STRUCTURE_2au4| PDB=2au4 | SCENE= }} | | {{STRUCTURE_2au4| PDB=2au4 | SCENE= }} |
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| - | '''Class I GTP aptamer'''
| + | ===Class I GTP aptamer=== |
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| - | ==Overview==
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| - | Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K(d) = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K(d) of 6 microM are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81%-85%). However, the GTP aptamer is more informationally complex (approximately 45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base-base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in K(d). These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_16510427}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 16510427 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_16510427}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU4 OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU4 OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Aptamer]] | | [[Category: Aptamer]] |
| | [[Category: Rna]] | | [[Category: Rna]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:28:46 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:24:01 2008'' |
Revision as of 20:24, 28 July 2008
Template:STRUCTURE 2au4
Class I GTP aptamer
Template:ABSTRACT PUBMED 16510427
About this Structure
Full experimental information is available from OCA.
Reference
Solution structure of an informationally complex high-affinity RNA aptamer to GTP., Carothers JM, Davis JH, Chou JJ, Szostak JW, RNA. 2006 Apr;12(4):567-79. Epub 2006 Feb 28. PMID:16510427
Page seeded by OCA on Mon Jul 28 23:24:01 2008
