Identification of protein/DNA contacts with dimethyl sulfate: methylation protection and methylation interference

Sequence-specific protein/DNA contacts direct most transcription factors to binding sites within the promoters of genes they regulate. Several chemical probes, such as dimethyl sulfate, have been used to obtain information on these sites of interaction. Protection and interference patterns frequently correspond to highly conserved positions within binding sites and are often specific for a given transcription factor or family of factors. The methods described here can be used to identify sites within a DNA sequence that are bound by nuclear factors or to characterise the contacts made by a purified factor or recombinant protein in vitro. As methylation protection is the in vitro equivalent of in vivo genomic footprinting, a direct comparison between in vivo and in vitro footprints can be made.