The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex

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.