title: The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex.
abstract: We examined, by 1H and 31P NMR, the solution structure of a 16 bp non-palindromic DNA fragment (16M2) containing the HIV-1 NF-kappaB-binding site, in which the sequences flanking the kappaB 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 kappaB fragment (16N) and a fragment in which mutations have been introduced at the 5' end of the kappaB site (16M1). For the mutated 16M2 duplex, NMR data showed that the BI-BII equilibrium, previously reported for the native fragment (16N) at the kappaB flanking steps, was lost. The role of the BI-BII equilibrium in NF-kappaB recognition by DNA was then investigated by electrophoretic mobility shift assay. We found that the isolated kappaB site has the potential to bind efficiently due to the BI-BII equilibrium of the kappaB flanking sequences.
authors.affiliation: Unité de RMN des Biomolécules, URA 2185 CNRS, Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris, France.
authors.forename: K
authors.initials: K
authors.lastname: Wecker
authors.forename: M C
authors.initials: MC
authors.lastname: Bonnet
authors.forename: E F
authors.initials: EF
authors.lastname: Meurs
authors.forename: M
authors.initials: M
authors.lastname: Delepierre
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000378:metabolism*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010755:Organophosphates / Q000737:chemistry; D010758:Phosphorus / Q000032:analysis*; D011485:Protein Binding
chemical_list: D046911:Macromolecular Substances; D016328:NF-kappa B; D010755:Organophosphates; D010758:Phosphorus; D004247:DNA