Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA

We have shown recently that the relative abundance of the three dimeric forms (alpha2, alphabeta and beta2) of the HU protein from Escherichia coli varies during growth and in response to environmental changes. Using gel retardation assays we have compared the DNA binding properties of the three dimers with different DNA substrates. The determination of their DNA binding parameters shows that the relative affinities of HUalphabeta and HUalpha2 are comparable. Both recognize, with a high degree of affinity under stringent conditions, cruciform structures or DNA molecules with a nick or a gap, whereas they bind to linear DNA only at low salt. DNA containing a gap of two nucleotides is in fact the substrate recognized with the highest degree of affinity by these two forms under all conditions. Conversely, HUbeta2 binds very poorly to duplex DNA and shows a much lower affinity for nicked or gapped DNAs. However, HUbeta2 binds to cruciform DNA structures almost as well as HUalphabeta and HUalpha2. This almost exclusive binding of HUbeta2 to a unique substrate is surprising in regards of the quasi identity, in the three forms, of the flexible arms considered as the DNA-binding domains of the three forms of HU. Cruciform DNA may stabilize HUbeta2 structure which could be structurally defective.