Characterizing IHF Binding to DNA Four-Way Junctions and Single-Stranded Forks

Integration Host Factor (IHF) is an architectural protein that binds and bends DNA, facilitating the formation of protein-DNA complexes important for gene regulation. IHF binds with high affinity to a specific consensus sequence in duplex DNA and induces a 160' bend upon binding. We have shown that IHF also binds DNA four way junctions (4WJ) that do not contain the consensus sequence with nanomolar affinity and 1:1 stoichiometry for the specific interaction. We have also observed that IHF binds DNA forks with nanomolar affinity. The binding to junctions and forks is in direct contrast to IHF binding to non-consensus linear duplex DNA, which is typically 1000-fold weaker. In this study we investigate whether the presence of the IHF consensus sequence influences IHF binding to DNA junctions and forks, as well as the structural features of these substrates that influence binding. We utilized gel shift and fluorescence binding assays to measure binding affinity and have observed that the high affinity for these non-native structures is independent of the presence of the consensus sequence. We have also identified structural features that appear to influence binding to forks. Through these measurements, we are also exploring whether the mechanism of recognition differs between junctions and forks.