The interaction of new 4,9-diazapyrenium compounds with double stranded nucleic acids

Abstract

Interactions of double stranded nucleic acids were studied with 4,9-diazapyrenium compounds, including monofunctional monocationic derivatives [4-methyl- (1) and 4-benzyl- (2)], monofunctional dicationic derivatives [4,9-dimethyl- with substituents H- (3) or Ph- (4) in the 5,10 positions and Me- (5) in the 2,7-positions], and bifunctional derivatives [4,4′-p- (6) and m- (7) xylylene bridged], which were described in the preceding paper. NMR spectra indicate intercalation for all ligands, with line width increases of up to 70 Hz. Thermal melting experiments and UV or fluorescence titrations were used to characterize affinities; these are essentially independent of the number of charges present in the ring systems, in line with negligible electrostatic binding contributions and with the corresponding affinities towards nucleotides (reported in the preceding paper). Substituents at the pyrenium rings have relatively little influence on the binding, with the exception of two phenyl groups, which lower the affinity, probably due to steric hindrance. Several melting curves are biphasic; in particular with the RNA-type polyA-polyU one observes transition points above and below the original denaturation point. Ligands containing two diazapyrenium rings bridged either by a m- or by a p-xylylene unit show distinctly higher affinities for the latter, and in Scatchard analyses a ligand to nucleotide ratio of n = 0.08, suggesting bisintercalation. Viscometry, however, shows a rather uniform length increase of the calf thymus DNA double helix with slopes of α = 1.1, similar to the known monointercalator ethidium bromide (α = 1.0). The monofunctional compounds exhibit some noteworthy RNA selectivity.