• DNA fragments must first be labeled at one end
• Treated with a chemical that modifies specific nucleotides, an
example being dimethyl sulphate, which attaches methyl groups to
guanine nucleotides
• DNA is mixed with the protein extract
• The key to the assay is that the binding protein will probably not
attach to the DNA if one of the guanines within the control region
is modified, because methylation of a nucleotide interferes with the
specific chemical reaction that enables it to form an attachment with
a protein
• unbound DNA is purified from the gel and treated with piperidine, a
chemical which cleaves DNA molecules at methylated nucleotides