Molecular size, shape, and electric charges: essential for perylene bisimide-based DNA intercalator to localize in cell nuclei and inhibit cancer cell growth.

The molecular properties concerning size, shape, and electric charges of the planar aromatic DNA intercalators are still poorly understood. Herein, a series of water-soluble perylene bisimide (PBI) derivatives containing a rigid and planar aromatic nanoscaffold with different size, shape, and electric charges were synthesized. Using histochemistry and cell viability assays on animal tissues and cancer cells, we revealed the molecular properties required for successful DNA intercalators to localize in cell nuclei and inhibit cancer cells. Small molecular size and the strong polarity of hydrophilic substituents are prerequisites for PBI-based DNA intercalators. A large number of charges facilitate the nucleic accumulation of these DNA intercalators, while fewer charges and planar aromatic nanoscaffold more efficiently inhibit cancer cell growth.