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Nucleic Acids Research, 2002, Vol. 30, No. 20 4452-4459
© 2002 Oxford University Press

The role of the phosphorus BI–BII transition in protein–DNA recognition: the NF-{kappa}B complex

K. Wecker, M. C. Bonnet1, E. F. Meurs1 and M. Delepierre*

Unité de RMN des Biomolécules, URA 2185 CNRS and 1 Unité de Virologie et d’Immunologie Cellulaire, URA 1930 CNRS, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 45 68 88 71; Fax: +33 1 45 68 89 29; Email: murield{at}pasteur.fr

We examined, by 1H and 31P NMR, the solution structure of a 16 bp non-palindromic DNA fragment (16M2) containing the HIV-1 NF-{kappa}B-binding site, in which the sequences flanking the {kappa}B site had been mutated. 31P NMR was particularly useful for obtaining structural information on the phosphodiester backbone conformation. Structural features were then compared with those of the two previously studied DNA fragments corresponding, respectively, to the native {kappa}B fragment (16N) and a fragment in which mutations have been introduced at the 5' end of the {kappa}B site (16M1). For the mutated 16M2 duplex, NMR data showed that the BI–BII equilibrium, previously reported for the native fragment (16N) at the {kappa}B flanking steps, was lost. The role of the BI–BII equilibrium in NF-{kappa}B recognition by DNA was then investigated by electrophoretic mobility shift assay. We found that the isolated {kappa}B site has the potential to bind efficiently due to the BI–BII equilibrium of the {kappa}B flanking sequences.


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