Bending and straightening of DNA induced by the same ligand: characterization with the atomic force microscope

A new ligand, MGT-6b, binds to DNA with two linked parts: a polyamine that binds to the phosphate backbone and a tripyrrole peptide that binds to the minor groove. This ligand decreases the curvature of bent kinetoplast DNA (kDNA) and also increases the curvature of a 400-bp DNA that is used as a molecular weight standard (M400), as characterized with the atomic force microscope (AFM). MGT-6b is more effective than distamycin at straightening kDNA. MGT-6b retards the electrophoretic mobility of M400 DNA, although neither of its two component parts alters the mobility of M400 or its curvature as seen in the AFM. Thus, both parts of the ligand are needed for the "vise grip" mode of binding that affects DNA bending. the ability of MGT-6b to both bend and straighten DNA is probably related to the very different DNA sequences and, hence, structures of kDNA and M400 DNA.