Sequence distribution and intercooperativity detection for two ligands simultaneously binding to DNA

A method for detecting and quantifying the cooperativity in the simultaneous binding of two ligands, A and B, to DNA (intercooperativity; ω AB ) is proposed. This involves the determination of an apparent affinity constant K app for one of the ligands (A) in the limit of its null saturation (ν A → 0), in the presence of the second one (B). A definition for this constant is given and an expression is derived corresponding to a simple model of competitive binding to an unbranched three‐state homogeneous polar lattice with nearest‐neighbor interactions (Markov chain). The ratio between the apparent and intrinsic affinity constants of one ligand in the maximum saturation limit of the other one becomes ω   2 AB , and thus can be graphically obtained from K   app Avs ν B plots. All the frequencies that define the sequence distribution of ligands can be easily calculated by introducing some generalized statistical weights for the free lattice monomer in a standard sequence generating function procedure. A model of fluorescence quenching emission is obtained from such frequencies under the hypothesis of a short‐range electron transfer mechanism of the deactivation; it confirms, as suggested by the binding model, an outstanding influence of the intercooperativity on the distribution. © 2001 John Wiley & Sons, Inc. Biopolymers 58: 562–576, 2001