The aggregation and G-quadruplex DNA selectivity of charged 3,4,9,10-perylenetetracarboxylic acid diimides.

Two N,N'-disubstituted perylene diimide G-quadruplex DNA ligands, Tel11 (N,N'-bis-[3-(4-methyl-morpholin-4-yl)-propyl]-3,4,9,10-perylenetetracarboxylic acid diimide diiodide) and Tel12 (N,N'-bis-[(3-phosphono)-propyl]-3,4,9,10-perylenetetracarboxylic acid diimide tetrapotassium salt) were synthesized and studied. Visible absorbance spectroscopy, resonance light scattering, and fluorescence spectroscopy were utilized to explore the aggregation state, affinity for various DNA structures, and G-quadruplex selectivity of these ligands. The water-soluble ligands exist in a monomer-dimer equilibrium with the cationic Tel11 exhibiting a greater affinity for various DNA structures than the anionic Tel12. Tel12 has greater selectivity for G-quadruplex DNA over double-stranded DNA than Tel11.