DNA-binding properties of 15-crown-5-derived mono- and bis-styryl dyes were investigated in the presence of calf thymus DNA. To access the factors that influence the DNA association in the series of these ligands, the structure of the molecules was varied by either changing size of the heterocyclic moiety or altering the position of the styryl substituents. The major binding mode for the monostyryl dyes is intercalation. Notably, binding of the dyes to the nucleic acids leads to a fluorescence enhancement by a factor of up to 54. Therefore, these cationic styryl derivatives may be applied as fluorescent “light-up” probes for DNA detection.

Biaryl derivatives that consist of one DNA-intercalating unit and a sterically demanding component exhibit a specific behavior towards abasic site-containing DNA (AP-DNA) as determined by thermal DNA denaturation experiments, spectrometric titrations and CD spectroscopic analysis. Specifically, these ligands strongly stabilize AP-DNA towards dissociation, whereas they do not or only marginally affect the melting temperature of regular duplex 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 a–c), 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 (K_b≈10⁶ M⁻¹) even in the absence of additional functional side chains. The binding modes of 4 a–c 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 π stacking of the diazoniachrysenes to the quadruplex is the major binding mode; however, because of different electron distributions of the π 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 π 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.

1,4-Dioxa-7,13-dithia-10-azacyclopentadecane (AT₂15C5) or 1,4,7,10-tetraoxa-13-azacyclopentadecane (A15C5) were attached as metal-ion-binding receptor units at the ortho or para positions of the 9-amino-N-phenylbenzo[b]quinolizinium chromophore. The addition of Hg²⁺ or Mg²⁺ to the para isomers of the AT₂15C5–quinolizinium or A15C5–quinolizinium conjugate, respectively, led to a blueshift of the absorption maxima of each compound because of the reduced donor ability of the complexed amino group. In contrast, the addition of Hg²⁺ to a solution of the ortho-AT₂15C5–quinolizinium conjugate in H₂O/MeOH mixtures induced a significant redshift (ca. 50 nm) of the absorption maximum and enabled the photometric discrimination between Hg²⁺ and competing thiophilic cations, such as Ag⁺ or Pb²⁺, because the latter, as well as other competing metal ions, did not induce such an effect. It is proposed that the Hg²⁺-induced redshift originates from the complexation of Hg²⁺ by the thiaazacrown ether followed by deprotonation of the secondary 9-amino substituent of the aminobenzoquinolizinium unit. The resulting amide functionality increases the donor–acceptor interplay leading to the redshifted absorption and also coordinates to Hg²⁺ to form a lariat ether type complex. A similar effect was observed upon the addition of Mg²⁺ to the 9-amino-N-phenylbenzo[b]quinolizinium derivative with the A15C5 unit in the ortho position; however, this effect was only operative in aprotic solvents, e.g. CH₃CN, and with less than 1 mol-equiv. of Mg²⁺.