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1k8j

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[[Image:1k8j.gif|left|200px]]
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{{STRUCTURE_1k8j| PDB=1k8j | SCENE= }}
{{STRUCTURE_1k8j| PDB=1k8j | SCENE= }}
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'''NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1'''
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===NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 12642125 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12642125}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8J OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8J OCA].
==Reference==
==Reference==
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[[Category: Dna duplex]]
[[Category: Dna duplex]]
[[Category: Nf-kb]]
[[Category: Nf-kb]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:25:59 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 09:56:57 2008''

Revision as of 06:57, 2 July 2008

Image:1k8j.png

Template:STRUCTURE 1k8j

NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1

Template:ABSTRACT PUBMED 12642125

About this Structure

Full experimental 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 Wed Jul 2 09:56:57 2008

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