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

A method for deterring and quantifying the cooperativity in the simultaneou s binding of two ligands, A and B, to DNA (intercooperativity: omega (AB)) is proposed. This involves the determination of an apparent affinity consta nt K-app for one of the ligands (A) in the limit of its null saturation (v( A) --> 0), in the presence of the second one (B). A definition for this con stant is given and an expression is derived corresponding to a simple model of competitive binding to an unbranched three-state homogeneous polar latt ice with nearest-neighbor interactions (Markov chain). The ratio between th e apparent and intrinsic affinity constants of one ligand in the maximum sa turation limit of the other one becomes omega (2)(AB), and thus can be grap hically obtained from K-A(aPP) vs V-B plots. All the frequencies that defin e the sequence distribution of ligands can be easily calculated by introduc ing some generalized. Statistical weights for the free lattice monomer in a standard sequence generating function procedure. A model of fluorescence q uenching 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 interc ooperativity on the distribution. (C) 2001 John Wiley & Sons, Inc.