1kbd

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[[Image:1kbd.gif|left|200px]]
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{{Seed}}
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{{STRUCTURE_1kbd| PDB=1kbd | SCENE= }}
{{STRUCTURE_1kbd| PDB=1kbd | SCENE= }}
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'''SOLUTION STRUCTURE OF A 16 BASE-PAIR DNA RELATED TO THE HIV-1 KAPPA B SITE'''
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===SOLUTION STRUCTURE OF A 16 BASE-PAIR DNA RELATED TO THE HIV-1 KAPPA B SITE===
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==Overview==
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1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.
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The line below this paragraph, {{ABSTRACT_PUBMED_9636705}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 9636705 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9636705}}
==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=1KBD OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBD OCA].
==Reference==
==Reference==
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[[Category: Modeling]]
[[Category: Modeling]]
[[Category: Nmr]]
[[Category: Nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:32:03 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 10:04:45 2008''

Revision as of 07:04, 2 July 2008

Image:1kbd.png

Template:STRUCTURE 1kbd

SOLUTION STRUCTURE OF A 16 BASE-PAIR DNA RELATED TO THE HIV-1 KAPPA B SITE

Template:ABSTRACT PUBMED 9636705

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex., Tisne C, Hantz E, Hartmann B, Delepierre M, J Mol Biol. 1998 May 29;279(1):127-42. PMID:9636705

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