Rational design of anthracene-based DNA binders.

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.

Novel enzyme/DNA/inorganic nanomaterials: a new generation of biocatalysts.

The design, synthesis and properties of a new class of enzyme/DNA/inorganic nanobiomaterials are described here. DNA has been used to stabilize the enzymes intercalated in the galleries of the inorganic solid, alpha-Zr(iv) phosphate (alpha-Zr(HPO(4))(2).H(2)O, abbreviated as alpha-ZrP). Interestingly, the presence of DNA improved the activity and stability of the bound enzymes. Key studies leading to the current strategy are presented initially, and these are followed by more recent developments. Several enzymes and proteins, including horseradish peroxidase, lysozyme, glucose oxidase, chymotrypsin, bovine serum albumin, cytochrome c, met-hemoglobin and met-myoglobin are successfully intercalated in the galleries of alpha-ZrP, under benign ambient conditions (aqueous buffered solutions, at room temperature and neutral pH). These novel materials are characterized by XRD, SEM and TEM as well as by biochemical, calorimetric and spectroscopic methods. Spectroscopic studies (circular dichroism, CD), for example, indicated that co-intercalation of DNA improved the retention of bound enzyme structure. The activity was enhanced markedly (five-fold) when DNA is co-intercalated, when compared to the activity in the absence of DNA. Addition of DNA to the sample, after enzyme intercalation, did not make any improvements. Our hypothesis is that enzyme-DNA supramolecular complex binds to the solid and the unfavorable interactions between the enzyme and the solid are minimized. These novel nanobiocomposite materials provide a simple method for packaging DNA and aid in engineering more effective synthetic materials for gene/RNA-delivery and drug delivery applications.