Sequence-influenced interactions of oligoacridines with DNA detected by retarded gel electrophoretic migrations

Abstract

We have found that di-, tri-, tetra-, and hexa-9-acridinylamines are so efficiently associated with DNA during electrophoresis in polyacrylamide or agarose gels that they retard its migration. The retardation is roughly proportional to the reagent to base pair ratio, and the magnitude of the retardation indicates that a combined charge neutralization/helix extension mechanism is mainly responsible for the effect. Furthermore, DNA sequence dependent differences are observed. Thus, the pUC 19 restriction fragments (HaeIII or AluI), which in the native state comigrate upon gel electrophoretic analysis, could be separated in the presence of a diacridine, and specific DNA fragments responded differently to different diacridines. These results suggest that the effect also is due to a contribution from the DNA conformation and that the DNA conformation dynamics are influenced differently upon binding of different diacridines. We foresee three applications of this observation: (1) in analytical gel electrophoretic separation of otherwise comigrating DNA molecules, (2) in studies of polyintercalator-DNA interaction, and (3) in measurements of polyintercalator-induced DNA unwinding.

Molecular mechanisms of DNA repair inhibition by caffeine.

“…Instead, it strongly promotes nonspecific binding by UvrA as evidenced by the striking protection of the whole fragment (damaged or undamaged) from DNase I digestion when both UvrA and caffeine are present. We can also detect caffeine-dependent binding of (20)(21)(22), and it appears to affect the DNase I digestion pattern in our experiments in the same way that other intercalating compounds affect DNase I digestion: producing a sequence specific enhancement or inhibition of digestion (23,24). These caffeine-enhanced or inhibited digestion sites are indicated by asterisks in Figs.…”

Synthesis, DNA interaction and cytotoxicity studies of cis-{[1, 2-bis(aminomethyl)cyclohexane]dihalo}platinum(II) complexes

“…The electrophoretic mobility of these two forms is very different and it depends on the degree of folding. The presence of the platinum compounds in the medium and their interaction with DNA can change the folding of these DNA forms [20][21][22][23][24].…”

Molecular Recognition of NADP(H) and ATP by Macrocyclic Polyamines Bearing Acridine Groups

“…Electrophoretic Mobility. The electrophoretic mobility [27] of supercoiled plasmid pBr322 on agarose gel in the presence of micromolar concentration of BA was strongly retarded. Acridin-9-amine, [24]-N,O,, or an equimolar mixture of the two at micromolar concentration had no effect on the migration ability of supercoiled plasmid pBr332 although it is known that polyamines [28] and acridine [25] derivatives interact strongly with double-stranded DNA.…”