Structural selectivity of drug-nucleic acid interactions probed by competition dialysis

Competition dialysis is a powerful new tool for the discovery of ligands that bind to nucleic acids with structural- or sequence- selectivity. The method is based on firm thermodynamic principles and is simple to implement. In the competition dialysis experiment, an array of nucleic acid structures and sequences is dialyzed against a common test ligand solution. After equilibration, the amount of ligand bound to each structure or sequence is determined spectrophotometrically. Since all structures and sequences are in equilibrium with the same free ligand concentration, the amount bound is directly proportional to the ligand binding affinity. Competition dialysis thus provides a direct and quantitative measure of selectivity, and unambiguously identifies which of the structures or sequences within the sample array are preferred by a particular ligand. Following the introduction of the method, competition dialysis has been used worldwide to probe a variety of ligand-nucleic acid interactions. This chapter will focus on new analytical approaches for extracting information from the database that resulted from the first-generation competition dialysis assay, in which binding data were gathered for the interaction of 126 compounds with 13 different structures and sequences. Such global analysis allows identification of compounds with unique types of binding selectivity.