2kbd: Difference between revisions
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'''5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'''' | '''5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'''' | ||
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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=2KBD OCA]. | |||
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/9636705 9636705] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/9636705 9636705] | ||
[[Category: Delepierre, M.]] | [[Category: Delepierre, M.]] | ||
[[Category: Hantz, E.]] | [[Category: Hantz, E.]] | ||
[[Category: Hartmann, B.]] | [[Category: Hartmann, B.]] | ||
[[Category: Tisne, C.]] | [[Category: Tisne, C.]] | ||
[[Category: | [[Category: Deoxyribonucleic acid]] | ||
[[Category: | [[Category: Dna structure]] | ||
[[Category: | [[Category: Modelling]] | ||
[[Category: | [[Category: Nmr]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 09:28:52 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 06:28, 4 May 2008
5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'
Overview
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.
About this Structure
Full crystallographic 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 Page seeded by OCA on Sun May 4 09:28:52 2008
