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

Interactions of double stranded nucleic acids were studied with 4,9-diazapy renium compounds, including monofunctional monocationic derivatives [4-meth yl- (1) and 4-benzyl- (2)], monofunctional dicationic derivatives [4,9-dime thyl- 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 spect ra indicate intercalation for all ligands, with line width increases of up to 70 Hz. Thermal melting experiments and UV or fluorescence titrations wer e used to characterize affinities; these are essentially independent of the number of charges present in the ring systems, in line with negligible ele ctrostatic binding contributions and with the corresponding affinities towa rds nucleotides (reported in the preceding paper). Substituents at the pyre nium rings have relatively little influence on the binding, with the except ion 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 origina l denaturation point. Ligands containing two diazapyrenium rings bridged ei ther 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 unifo rm length increase of the calf thymus DNA double helix with slopes of alpha = 1.1, similar to the known monointercalator ethidium bromide (alpha = 1.0 ). The monofunctional compounds exhibit some noteworthy RNA selectivity.