1k8n: Difference between revisions
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[[Image:1k8n.gif|left|200px]] | [[Image:1k8n.gif|left|200px]] | ||
'''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24''' | {{Structure | ||
|PDB= 1k8n |SIZE=350|CAPTION= <scene name='initialview01'>1k8n</scene> | |||
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'''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1K8N is a [ | 1K8N 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=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:// | 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://www.ncbi.nlm.nih.gov/pubmed/12642125 12642125] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Bassett, S E.]] | [[Category: Bassett, S E.]] | ||
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[[Category: xby6]] | [[Category: xby6]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:13:59 2008'' | ||
Revision as of 10:13, 20 March 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
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