Tuning the DNA binding modes of an anthracene derivative with salt

The DNA binding properties of an anthracene derivative with substituents at the 9 and 10 positions, carrying four positive charges, are examined in calorimetric, spectroscopic and photocleavage studies. Isothermal titration calorimetric data indicated exothermic binding of the ligand to calf thymus DNA with a binding constant of (1.4 +/- 0.5) x 10(5) M-1 and this value is much greater than binding of similar monocationic derivatives. The values for the other binding parameters were, Delta H = -3.5 +/- 0.4 kcal/mol; Delta S = 11.6 +/- 1.6 cal/mol K, and a binding site size of similar to 4 base pairs. Absorption spectral studies indicated small, but significant red shifts in the vibronic bands, and similar to 70% of hypochromism. The binding plots indicated bi-phasic binding of the ligand. At higher ionic strengths, the red shifts in the absorption spectra were abolished but significant hypochromism persisted. Excitation and sensitized fluorescence spectral studies indicated weak energy transfer from the DNA bases to the ligand. Further more, energy transfer was reduced substantially at higher ionic strengths. Strong induced circular dichroism bands are noted, in the 300-400 nm region, and these are most likely dominated by the contributions from the groove bound form as well as the intercalated chromophore. Helix melting studies indicated improvement in the helix stability, and substantial increase in the melting temperature (Delta T-m > 17 degrees C). Differential scanning calorimetric data, on the other hand, indicated only minor improvements in the thermodynamic parameters. Irradiation of a mixture of the ligand (2 mu M) and supercoiled pUC18 DNA (20 mu M, @374 nm) resulted in the efficient formation of nicked circular DNA (> 90%) in an hour. The data indicated at least two distinct binding modes, and one of these persisted at high ionic strengths (375 mM NaCl). Substitution at 9 and 10 positions of the anthracene ring system with positively charged residues resulted in multiple binding modes, and these are resolvable in ionic strength studies. (c) 2005 Elsevier B.V. All rights reserved.