Threading Intercalators as a New DNA Structural Probe

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Abstract
Nogalamycin is a threading intercalator and when it binds with double stranded DNA, one of the two sugar substituents goes between adjacent base pairs of DNA to form a stable complex in which the two substituents of nogalamycin are projecting out in each groove of DNA. Since the molecular volume of the substituents of nogalamycin is larger than that of the space created through the motion of DNA strands constituting the double helix, a cleavage of hydrogen bonds in the base pairs of DNA duplex is necessary to form such a complex. The structure of double-stranded DNA is dynamic, and the base pair cleavage (base pair opening) and re-formation (closing) occur frequently at ambient temperature. A wider variety of threading intercalators is obtainable synthetically, and they include several families such as 1,5-disubstituted anthraquinones, 9,10-disubstituted anthracenes, and naphthalene bis(dicarboximide) derivatives. Kinetic study of the complex formation and dissociation of naphthalene bis(dicarboximide) carrying substituents of different size have made one recognize the dynamic character of duplex DNA in intercalation reaction. A cyclic bis-intercalator was also able to form a threading complex of a catenane-like structure. A thorough study of the binding behavior of natural and synthetic threading intercalators with DNA revealed that a proper design of substituents on threading intercalators can produce ligands which specifically bind either to single- or double-stranded DNA. These ligands, synthetic ones in particular, will hopefully serve not only as new DNA structural probes but also as chemotherapeutic agents.