Methyl green. A DNA major-groove binding drug.

Interaction and binding geometries of complexes of Methyl green with poly(dA-dT)2, poly(dA).poly(dT), and triplex poly(dA).2poly(dT) complexes have been studied by linear dichroism. For both of the complexes with double helical DNAs, the z symmetry axis of Methyl green is found to be approximately parallel to the DNA bases while the x symmetry axis lies at 40-44 degrees relative to the local DNA helix axis, in agreement with a groove binding mode. However, in contrast to minor-groove binders (such as DAPI and Hoechst 33258) Methyl green is found to be excluded from binding to the triple helical poly(dA).2poly(dT) in which the major groove is filled by the third strand. While most so far studied groove-binding dyes bind in the minor groove of DNA, Methyl green thus appears to be an exception.