DNA Intercalators: Cutting plasmids in half

We have designed and synthesized novel intercalating compounds that efficiently hydrolyze supercoiled plasmid DNA lacking depurine/depyrimidine sites. These intercalators consist of conjugates of diamine and thia-heterocyclic naphthalimide. Surprisingly, the initial hydrolyzed products comprised fragments with half the length of the original plasmid. We suggest a mechanochemical mechanism that explains this ‘1/2 rule’. The higher the intercalators’ ability to bind to DNA, the more efficient was the cleavage and the higher the yield of half-sized cleavage products. Analysis of the relationship between structure and function suggests that planar aromatic heterocycles and amino side chains promote DNA cleavage via intercalation and electrostatic binding. The 1/2 rule phenomenon provides new insights into the molecular mechanism by which these compounds sever DNA through binding and cooperative effects. INTRODUCTION Small molecules that can hydrolyze DNA or RNA are important in biotechnology and medicine(1-4).Simple organic amines are known as RNA cleavers (5-7). Compared with monoamines, aliphatic diand polyamines accelerate the cleavage of ApA up to two orders of magnitude at 50C (7). They also degrade poly(A), poly(U), and poly(C), but not poly(G), into fragments shorter than pentamers (6). Tethering the amine to an intercalator enhances their RNA cleaving activity(8). This cleavage process has been proved to be ! elimination to generate 3'-OH and 5'-P termini (9-12). Under certain conditions, amines can also act as DNA cleavers. For example, metallic cation complexes containing aliphatic dior polyamines, the intercalative anthraquinone or acridine-based aminoalkyl amide, have been reported to degrade DNA via hydrolysis (13-24).On the other hand, amines themselves can cleave at apurinic or apyrimidinic DNA sites (where the N-glycosidic bond that connects the nucleic base to the deoxyribose moiety is