Shape-independent model (SHIM) approach for studying aggregation by NMR diffusometry.

NMR diffusometry has been gaining wide popularity in various areas of applied chemistry for investigating diffusion and complexation processes in solid and aqueous phases. To date, the application of this method to study aggregation phenomena proceeding beyond the dimer stage of assembly has been restricted by the need for a priori knowledge of the aggregates' shape, commonly difficult to know in practice. We describe here a comprehensive analysis of aggregation parameter-dependency on the type and shape selected for modeling assembly processes, and report for the first time a shape-independent model (designated the SHIM approach), which may be used as an alternative in cases when information on aggregates' shapes is unavailable. The model can be used for determining equilibrium aggregation parameters from self-diffusion NMR data including equilibrium self-association constant and changes in enthalpy, ΔH, and entropy, ΔS.

Energetics of ligand binding to the DNA minor groove.

In the present work the decomposition of the total Gibbs free energy of ligand-DNA binding onto various physical terms was accomplished for the group of nine DNA minor groove binders (MGB ligands) differing in both structure and charge state. The decomposition protocol includes the analysis of the most complete set of physical factors known to contribute to the complexation process, viz. the net change in the number of degrees of freedom (translational, rotational, vibrations of the chemical bonds and vibrations of the ligand as a whole within the binding site), the conformational entropy, van der Waals, electrostatic and hydrophobic interactions, the polyelectrolyte contribution and the net effect of changes in the number of hydrogen bonds. All of these processes are further decomposed into the interaction with the solvent and the interaction of the ligand with DNA. The principal outcome of the decomposition is the possibility of performing a comparative analysis of the energetic contribution of various physical terms and provide an answer to the question concerning what physical factors stabilize or destabilize the complexes of MGB ligands with DNA.