Compaction of single DNA molecules induced by binding of integration host factor (IHF)

We studied the interaction between the integration host factor (IHF), a maj or nucleoid-associated protein in bacteria, and single DNA molecules. Force -extension measurements of lambda DNA and an analysis of the Brownian motio n of small beads tethered to a surface by single short DNA molecules, in eq uilibrium with an IHF solution, indicate that: (i) the DNA-IHF complex reta ins a random, although more compact, coiled configuration for zero or small values of the tension, (ii) IHF induces DNA compaction by binding to multi ple DNA sites with low specificity, and (iii) with increasing tension on th e DNA, the elastic properties of bare DNA are recovered. This behavior is c onsistent with the predictions of a statistical mechanical model describing how proteins bending DNA are driven off by an applied tension on the DNA m olecule. Estimates of the amount of bound IHF in DNA-IHF complexes obtained from the model agree very well with independent measurements of this quant ity obtained from the analysis of DNA-IHF crosslinking. Our findings suppor t the long-held view that IHF and other histone-like proteins play an impor tant role in shaping the long-scale structure of the bacterial nucleoid.