Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference

Dimethyl sulfate (DMS) is an effective and widely used probe for sequence-specific protein-DNA interactions. It is the only probe routinely used both for in vitro (methylation protection, methylation interference) and in vivo (DMS genomic footprinting) applications since it rapidly reacts with DNA at room temperature and readily penetrates intact cells (1 ). DMS predominantly methylates the 7-nitrogen of guanine and 3-nitrogen of adenine. Thus, reactivity with G residues occurs in the major groove and with A residues in the minor groove. In standard Maxam and Gilbert protocols (2 ), the methylated bases are subsequently converted to strand breaks and displayed on sequencing gels.