1k8n: Difference between revisions
New page: left|200px<br /><applet load="1k8n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k8n" /> '''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANA... |
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[[Image:1k8n.gif|left|200px]]<br /><applet load="1k8n" size=" | [[Image:1k8n.gif|left|200px]]<br /><applet load="1k8n" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1k8n" /> | caption="1k8n" /> | ||
'''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24'''<br /> | '''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24'''<br /> | ||
==Overview== | ==Overview== | ||
A variety of monothio- and dithiosubstituted duplex aptamers targeting | A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone. | ||
==About this Structure== | ==About this Structure== | ||
1K8N 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:// | 1K8N 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8N OCA]. | ||
==Reference== | ==Reference== | ||
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB., Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG, Bioorg Chem. 2002 Dec;30(6):396-419. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12642125 12642125] | Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB., Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG, Bioorg Chem. 2002 Dec;30(6):396-419. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12642125 12642125] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Bassett, S | [[Category: Bassett, S E.]] | ||
[[Category: Fennewald, S | [[Category: Fennewald, S M.]] | ||
[[Category: Gorenstein, D | [[Category: Gorenstein, D G.]] | ||
[[Category: Herzog, N.]] | [[Category: Herzog, N.]] | ||
[[Category: King, D | [[Category: King, D J.]] | ||
[[Category: Luxon, B | [[Category: Luxon, B A.]] | ||
[[Category: Venkitachalam, S.]] | [[Category: Venkitachalam, S.]] | ||
[[Category: Volk, D | [[Category: Volk, D E.]] | ||
[[Category: Yang, X.]] | [[Category: Yang, X.]] | ||
[[Category: ck1]] | [[Category: ck1]] | ||
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[[Category: xby6]] | [[Category: xby6]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:31:18 2008'' | ||
Revision as of 11:31, 21 February 2008
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NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24
Overview
A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.
About this Structure
1K8N is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB., Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG, Bioorg Chem. 2002 Dec;30(6):396-419. PMID:12642125
Page seeded by OCA on Thu Feb 21 13:31:18 2008
