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Nucleic Acids Research, 1995, Vol. 23, No. 15 2959-2965
© 1995

METHODS

In vivo interaction of the Excherichia coli integration host factor with its specific binding sites

Manuel Engelhorn, Freédeéric Boccard+, Christine Murtin, Pierre Prentki{dagger} and Johannes Geiselmann*

Department of Molecular Biology, University of Geneva 30 Quai Emest Ansermet, 1211 Geneva 4, Switzerland

*To Whom correspondence should be addressed

Received April 4, 1995. Accepted July 4, 1995.

The histone-like protein integration host factor (IHF) of Escherichia coll binds to specific binding sites on the chromosome or on mobile genetic elements, and is involved in many cellular processes. We have analyzed the interaction of IHF with five different binding sites In vitro and in vivo using UV laser footprinting, a technique that probes the immediate environment and conformation of a segment of DNA. Using this generally applicable technique we can directly compare the binding modes and Interaction strengths of a DNA binding protein in its physiological environment within the cell to measurements performed in vitro. We conclude that the interactions between IHF and its specific binding sites are identical In vitro and In vivo. The footprinting signal is consistent with the model of IHF-binding to DNA proposed by Yang and Nash(1989). The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell.

+Present address: Laboratorie de Chimie Bacteérienne, UPR7221, CNRS, 31 ch. J.Aiguier, 13009 Marseille, France

{dagger}Decessed July 24, 1993


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