The assembly of the complex nucleoprotein arrays that govern DNA metabolism is often limited by the inherent stiffness of the duplex. The IHF protein of E. coli is representative of a group of proteins dedicated to overcoming this limitation by introducing points of DNA bending at strategic places in the genome. We have evaluated the degree to which non-specific DNA binding influences the biological availability of IHF protein. By combining in vitro measurement of affinity and in vivo footprinting we have determined that non-specific interactions severely reduce the effective intracellular concentration of the protein, thereby permitting high affinity IHF binding sites to serve as landmarks. We have also prepared co-crystals of IHF and one such specific binding site, opening the way for the determination of the molecular structure of this complex. In related work, we have shown that a one segment of DNA can be assembled by IHF and a recombination protein, Int, into two alternative architectures. By using the same IHF site but a different set of binding sites for Int, the 100 bp segment is thereby activated to undergo recombination with two different partners. Int protein catalyzes recombination of bacteriophage lambda using a topoisomerase mechanism. Abortive recombination can damage the host chromosome by trapping a covalent intermediate between Int and DNA; eukaryotic topoisomerases are subject to the same danger. We have discovered a novel phosphodiesterase activity that can function as a DNA repair enzyme for this damage.
