In vivo UV-laser footprinting

Abstract This chapter describes the use of UV-laser footprinting for detecting protein DNA interactions within a living bacterial cell. The principle of UV-laser footprinting is described in Chapter 14, and we concentrate on protocols that specifically address the extension of the technique to in vivo experiments. DNA-binding proteins exert their function when they associate with a specific DNA target. The biological activity of such c1 protein is therefore a direct function of the saturation of the specific DNA-binding site with the protein. The question that we want to answer, using UV-laser footprinting in vivo, is: ‘to what extend is a specific site on the DNA saturated by the protein that binds this sequence?’