Initially DNA fragments are 32p end labeled after which guanine and adenine nucleotides are methylated by treatment with dimethyl sulfate. Treatment with this chemical generally results in 1 modified base per DNA molecule (1). Next the protein of interested is incubated with the methylated DNA fragment. If the DNA is modified at nucleotides that are involved in protein binding, the protein will be unable to bind to the DNA. However, if methylation has occurred at nucleotides that are not important to protein binding, the protein will be able to bind to the DNA (1). DNA fragments that are bound by protein and those that are not bound by protein can be separated via electrophoretic mobility shift assay. Other common techniques used to separate bound and unbound DNA fragments include filter binding and immunoprecipitation (1). Next the DNA molecules are treated with an enzyme, such as piperidine, which will cleave the DNA molecules into smaller fragments. Piperidine cleaves DNA at modified bases. Finally the fragments are run on a denaturing gel along with a sequencing ladder. Because each DNA molecule is only methylated at a single position the sequencing ladder can be used to determine which nucleotide had been modified. Cleavage fragments that are generated from unbound DNA will differ from the fragments generated from DNA that was bound by protein. Thus the fragments generated from bound or unbound DNA can be used to determine the nucleotides that are important in protein binding.