Characterization of the binding of HU and IHF, homologous histone-like proteins of Escherichia coli, to curved and uncurved DNA

The binding of E, coli histone-like protein HU to curved and uncurved DNA fragments containing adenine tracts was characterized by relative binding affinity assay, and compared with that of other homologous histone-like protein integration host factor (IHF). Both HU and IHF have about 3- to 5-fold higher affinity for overall curved DNA fragments such as (A(6)N(4))(11) and (A(3)T(3)N(4))(12) compared to a standard duplex fragment with mixed sequence. The binding manner of HU to the curved fragments was highly cooperative. However, loss of overall curvature for shorter fragments (< similar to 100 bp) reduced the preference of HU binding to curved (A(3)T(3)N(4))(n) over uncurved (T(3)A(3)N(4))(n), indicating that the binding specificity of HU to curved DNA is length-dependent, Thus, the curved DNA configuration of the whole molecule facilitates the binding of several HU molecules to form the hierarchy of HU-DNA complex. Furthermore, it was shown that HU and IHF bind less well to (A(6)N(9))(n), which has a zig-zag straight structure, whereas they preferentially bind to uncurved (T(3)A(3)N(4))(14). These results suggested that not only intrinsically overall curvature but also the preferred orientations for DNA bending in the protein-DNA complex are important factors for affinities of HU and MF.