Competitive cooperative bindings of a small ligand to a linear polymer. II. Investigations on the mechanisms of proflavine binding to poly (A) and DNA.

Experimental binding isotherms relative to the interactions between proflavine and poly(A) or DNA are analyzed by comparison with theoretical models dealing with competitive cooperative bindings. In the case of poly(A), there are apparently no specific binding sites for the positive co-operative binding (complex I) leading to dye aggregation along the polyanionic chain. The second complex (complex II) seems to involve specific base-dye interactions, but it cannot be said whether this binding displays negative cooperativity or noncooperativity. None of the two simpler theoretical models agree quantitatively with all experimental data. A plausible interpretation can be given if it is assumed that (i) the electrostatic binding of one isolated bound dye molecule (nucleus of complex I) involves a definite interaction between a phosphate group and the positive charge of the dye; (ii) the structure of complex II is such that a dye–phosphate ionic interaction is maintained. In the case of DNA, our model of monoexclusive interactions fits the data more closely than does the model of biexclusive interactions. This gives experimental support for structural models in which the intercalated molecule interacts preferentially with one strand of the double helix and blocks only one phosphate for electrostatic binding. In order to propose a mechanism consistent with equilibrium and relaxation kinetic data, a modified reaction scheme is considered which takes account of the cooperativity effects in external binding and extends previous models.     

EQUIL: Simulation and data analysis of binding reactions with arbitrary chemical models

We have developed an algorithm for simulation and analysis of arbitrary chemical systems in equilibrium, with emphasis on ligand binding reactions. The program EQUIL can treat reactions involving multiple ligands, multiple binding sites, ternary complex models, allosteric effectors, competitive and noncompetitive binding, conformational changes, cooperativity, and generally any scheme that can be represented as a set of chemical equations. EQUIL is based on a general thermodynamic model of chemical equilibria; it does not involve nonlinear transformation of experimental data, but it does require the user to define the model of interaction between ligands and receptors by writing down the appropriate chemical reactions. EQUIL contains features of particular importance to ligand binding experiments: variable binding capacities, nonspecific binding, and the ability to simultaneously analyze data from different types of experiments. Furthermore, the simulation feature of EQUIL allows the user to investigate the feasibility of experiments that could possibly distinguish between different reaction models. We illustrate the use of this program on personal computers to analyze and simulate simple and complicated interactions between ligands and receptors.