Rational Design of Anthracene-Based DNA Binders

Abstract

Achieving the goal of rational design of DNA-binding ligands is important, and many inroads have been made in this direction. Toward that goal, we report a simple, systematic, and quantitative approach to design DNA-binding anthracene derivatives. Current data show that the binding free energies (DeltaG degrees) as well as enthalpies (DeltaH degrees) are related to specific structural features of the binders. Systematic design of anthracene probes, for example, indicated that the affinity can be enhanced via the introduction of methylene groups. Each methylene group contributed, on an average, -0.08+/-0.002 kcal/mol (at 1 M ionic strength, 293 K) toward the total binding free energy. Binding of the probes to DNA depended on ionic strength, and ionic strength studies were used to factor out to parse free-energy contributions due to specific interactions. The intrinsic free-energy contributions (DeltaGMol) of the probes are obtained by factoring out contributions from ionic interactions, hydration, conformational changes, polyelectrolyte effect, and the loss of rotational/translational motion. A strong, linear correlation was noted between DeltaGMol and the number of methylene groups present in the probe, and the correlation indicated free-energy contributions of -1.49 kcal/mol per methylene (at 50 mM NaCl, 293 K). This important observation provides a convenient handle to systematically fine-tune the intrinsic affinities of DNA binders. DeltaH values also showed clear trends, and each methylene contributed +0.28 kcal/mol toward the overall binding enthalpy (at 50 mM NaCl, 293 K), and this aspect is useful to fine-tune DeltaH contributions to binding. These important physical insights, derived from systematic modifications of the side chains of the DNA binders, are useful in the rational design of novel DNA binders.