Two distinct thermal stabilities of DNA and enzymatic activities of DNase I in a multistep assembly with carbazole ligands: different binding characteristics for duplex and quadruplex DNA

A partially hydrophobic carbazole ligand ((Im(+))2Cz: 2,2'-(9-ethyl-9 H-carbazole-3,6-diyl)bis(ethyne-2,1-diyl)bis(1,3-dimethyl-1H-imidazol-3-ium)) adopts two different binding states (binding states I and II) in its interactions with calf-thymus (ct-) DNA. Two distinct binding states were identified by biphasic UV/Vis and circular dichroism (CD) spectral changes during the titration of DNA into the carbazole ligand. At low concentrations of ct-DNA, (Im(+))2Cz binds to nearly every part of ct-DNA (binding state I). By contrast, an increased concentration of ct-DNA results in a switch in the DNA-binding state, so that the ligands are bound per five DNA base pairs. Similarly, a monocationic carbazole ligand (Im(+)Cz: 2-((6-bromo-9-ethyl-9 H-carbazol-3-yl)ethynyl)-1,3-dimethyl-1H-imidazol-3-ium) also shows biphasic UV/Vis spectral changes during the titration of ct-DNA into Im(+)Cz, which suggests two different binding states of the Im(+)Cz ligand with ct-DNA. The stepwise equilibrium of the ligand-DNA-complex formation is capable of switching the thermal stability of ct-DNA, as well as the enzymatic activity of deoxyribonuclease (DNase I). In binding state I, the (Im(+))2Cz ligands interact with nearly every base pair in ct-DNA and stabilize the double-helix structure, which results in a larger increase in the melting temperature of the ct-DNA than that observed with binding state II. On the other hand, the (Im(+))2Cz ligand significantly reduces the enzymatic activity of DNase I in binding state I, although the enzymatic activity is recovered once the binding state of the ligand-DNA complex is changed to binding state II. The (Im(+))2Cz ligand was also employed as a binder for G-quadruplex DNA. In contrast to the stepwise complex formation between (Im(+))2Cz and ct-DNA, (Im(+))2Cz shows a monotonous UV/Vis spectral response during the titration of G-quadruplex DNA into (Im(+))2Cz, which suggests a single binding state for (Im(+))2Cz with G-quadruplex DNA.