Polycyclic Azoniahetarenes: Assessing the Binding Parameters of Complexes between Unsubstituted Ligands and G-Quadruplex DNA

Polycyclic azoniahetarenes were employed to determine the effect of the structure of unsubstituted polyaromatic ligands on their quadruplex-DNA binding properties. The interactions of three isomeric diazoniadibenzo[b,k]chrysenes (4?ac), diazoniapentaphene (5), diazoniaanthra[1,2-a]anthracene (6), and tetraazoniapentapheno[6,7-h]pentaphene (3) with quadruplex DNA were examined by DNA melting studies (FRET melting) and fluorimetric titrations. In general, penta- and hexacyclic azoniahetarenes bind to quadruplex DNA (Kb similar to 106?M-1) even in the absence of additional functional side chains. The binding modes of 4?ac and 3 were studied in more detail by ligand displacement experiments, isothermal titration calorimetry, and CD and NMR spectroscopy. All experimental data indicate that terminal p stacking of the diazoniachrysenes to the quadruplex is the major binding mode; however, because of different electron distributions of the p systems of each isomer, these ligands align differently in the binding site to achieve ideal binding interactions. It is proposed that tetraazonia ligand 3 binds to the quadruplex by terminal stacking with a small portion of its p system, whereas a significant part of the bulky ligand most likely points outside the quadruplex structure, and is thus partially placed in the grooves. Notably, 3 and the known tetracationic porphyrin TMPyP4 exhibit almost the same binding properties towards quadruplex DNA, with 3 being more selective for quadruplex than for duplex DNA. Overall, studies on azonia-type hetarenes enable understanding of some parameters that govern the quadruplex-binding properties of parent ligand systems. Since unsubstituted ligands were employed in this study, complementary and cooperative effects of additional substituents, which may interfere with the ligand properties, were eliminated.