Filter-binding assays.

Structural studies of DNA-protein complexes reveal networks of contacts between proteins and the phosphates, sugars and bases of DNA. Our understanding of these structures, especially at the usual level of resolution for complexes between proteins and DNA (1.5-3.0 A), is not sufficient to be able to infer directly the relative contributions of each contact to the overall binding energy. A range of biochemical methods have therefore been developed in order to probe the relative affinities of proteins for particular DNA target sites in vitro. Of these, one of the easiest and most widely used is nitrocellulose filter-binding. By exploiting the differential adsorption to nitrocellulose of proteins and peptides compared to nucleic acids, it is possible to prepare equilibrium mixtures of the proteins and nucleic acids of choice and estimate the amount of complex formation by rapid filtration. The concentration dependence of binding yields estimates of the equilibrium dissociation constant and trivial variations allow access to kinetic and thermodynamic data. The use of this technique is illustrated here using results from our experiments with the Escherichia coli methionine repressor, MetJ.