title: Methyl green and its analogues bind selectively to AT-rich regions of native DNA.
abstract: Methyl green has long been used as a DNA stain in histochemistry. The sequence selective binding of the cationic triphenylmethane dyes methyl green, crystal violet and Malachite green to DNA was investigated by DNAase 1 and micrococcal nuclease footprinting. At low concentrations the ligands showed similar footprinting patterns which centred around AT-rich regions with a mild preference for hompolymeric A and T. At higher concentrations the dyes bound to almost all available DNA sites. Models, with and without intercalation are discussed to account for the specific binding.
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D003850:Deoxyribonuclease I; D005840:Gentian Violet / Q000737:chemistry / Q000378:metabolism; D066298:In Vitro Techniques; D008739:Methyl Green / Q000737:chemistry / Q000378:metabolism*; D008836:Micrococcal Nuclease; D008969:Molecular Sequence Data; D012394:Rosaniline Dyes / Q000737:chemistry / Q000378:metabolism
chemical_list: D012394:Rosaniline Dyes; C005095:malachite green; D008739:Methyl Green; D004247:DNA; D003850:Deoxyribonuclease I; D008836:Micrococcal Nuclease; D005840:Gentian Violet